Genome Analysis Toolkit

Leslie Youtsey · August 31, 2022 19:31

REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

REQUIRED for all errors and issues:
a) GATK version used: GATK version used: gatk-4.2.6.1

b) Exact command used:

#!/bin/bash

#PBS -l nodes=1:pamunkey:ppn=24

#PBS -l walltime=30:00:00

#PBS -N ASE

#PBS -o /ches/data10/lgspeight/results/ASE/ASE_output

#PBS -e /ches/data10/lgspeight/results/ASE/ASE_error

#PBS -t 1-48%3

REF=/ches/data10/lgspeight/RNA-Seq/01_rawdata/genome/Clam_genome.fna

/ches/home00/lgspeight/gatk-4.2.6.1/gatk CreateSequenceDictionary -R $REF

WORKDIR=/ches/data10/lgspeight/results/ASE

cd $WORKDIR

BAMDIR=/ches/data10/lgspeight/results/Align

VCFDIR=/ches/data10/lgspeight/results/SNP_Call/SNPS

ACCLIST=/ches/data10/lgspeight/RNA-Seq/01_rawdata/accessionlist.txt

NUM=$(expr ${PBS_ARRAYID})

SAMPLE=$(sed -n ${NUM}p $ACCLIST)

/ches/home00/lgspeight/gatk-4.2.6.1/gatk IndexFeatureFile -I $VCFDIR/$SAMPLE-var.final.vcf.gz

PICARD=/ches/home00/lgspeight/picard-2.27.4/picard/build/libs/picard.jar

java -jar $PICARD AddOrReplaceReadGroups \

I=$BAMDIR/${SAMPLE}.bam \

O=$BAMDIR/${SAMPLE}.2.bam \

RGID=4 \

RGLB=lib1 \

RGPL=ILLUMINA \

RGPU=unit1 \

RGSM=20

/ches/home00/lgspeight/gatk-4.2.6.1/gatk --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' ASEReadCounter \

-R $REF \

-I $BAMDIR/${SAMPLE}.2.bam \

-V $VCFDIR/$SAMPLE-var.final.vcf.gz \

-O $WORKDIR/${SAMPLE}.table

c) Entire program log:

Using GATK jar /ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar

Running:

java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar CreateSequenceDictionary -R /ches/data10/lgspeight/RNA-Seq/01_rawdata/genome/Clam_genome.fna

INFO 2022-08-25 10:10:29 CreateSequenceDictionary Output dictionary will be written in /ches/data10/lgspeight/RNA-Seq/01_rawdata/genome/Clam_genome.dict

10:10:29.453 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so

[Thu Aug 25 10:10:29 EDT 2022] CreateSequenceDictionary --REFERENCE /ches/data10/lgspeight/RNA-Seq/01_rawdata/genome/Clam_genome.fna --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false

[Thu Aug 25 10:10:29 EDT 2022] Executing as lgspeight@pm01.hpc.vims.edu on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_292-b10; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.2.6.1

[Thu Aug 25 10:10:29 EDT 2022] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.

Runtime.totalMemory()=2151153664

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

picard.PicardException: /ches/data10/lgspeight/RNA-Seq/01_rawdata/genome/Clam_genome.dict already exists. Delete this file and try again, or specify a different output file.

at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:220)

at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)

at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

at org.broadinstitute.hellbender.Main.main(Main.java:289)

Using GATK jar /ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar

Running:

java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar IndexFeatureFile -I /ches/data10/lgspeight/results/SNP_Call/SNPS/A_1_32-var.final.vcf.gz

10:10:32.889 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so

10:10:33.058 INFO IndexFeatureFile - ------------------------------------------------------------

10:10:33.058 INFO IndexFeatureFile - The Genome Analysis Toolkit (GATK) v4.2.6.1

10:10:33.059 INFO IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/

10:10:33.059 INFO IndexFeatureFile - Executing as lgspeight@pm01.hpc.vims.edu on Linux v3.10.0-514.el7.x86_64 amd64

10:10:33.059 INFO IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_292-b10

10:10:33.059 INFO IndexFeatureFile - Start Date/Time: August 25, 2022 10:10:32 AM EDT

10:10:33.059 INFO IndexFeatureFile - ------------------------------------------------------------

10:10:33.060 INFO IndexFeatureFile - ------------------------------------------------------------

10:10:33.060 INFO IndexFeatureFile - HTSJDK Version: 2.24.1

10:10:33.060 INFO IndexFeatureFile - Picard Version: 2.27.1

10:10:33.061 INFO IndexFeatureFile - Built for Spark Version: 2.4.5

10:10:33.061 INFO IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2

10:10:33.061 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

10:10:33.061 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

10:10:33.061 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

10:10:33.061 INFO IndexFeatureFile - Deflater: IntelDeflater

10:10:33.061 INFO IndexFeatureFile - Inflater: IntelInflater

10:10:33.062 INFO IndexFeatureFile - GCS max retries/reopens: 20

10:10:33.062 INFO IndexFeatureFile - Requester pays: disabled

10:10:33.062 INFO IndexFeatureFile - Initializing engine

10:10:33.062 INFO IndexFeatureFile - Done initializing engine

10:10:33.581 INFO FeatureManager - Using codec VCFCodec to read file file:///ches/data10/lgspeight/results/SNP_Call/SNPS/A_1_32-var.final.vcf.gz

10:10:33.682 INFO ProgressMeter - Starting traversal

10:10:33.683 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute

10:10:39.116 WARN IntelInflater - Zero Bytes Written : 0

10:10:39.119 INFO ProgressMeter - NW_025543028.1:13539 0.1 755807 8346847.0

10:10:39.119 INFO ProgressMeter - Traversal complete. Processed 755807 total records in 0.1 minutes.

10:10:39.201 INFO IndexFeatureFile - Successfully wrote index to /ches/data10/lgspeight/results/SNP_Call/SNPS/A_1_32-var.final.vcf.gz.tbi

10:10:39.202 INFO IndexFeatureFile - Shutting down engine

[August 25, 2022 10:10:39 AM EDT] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.11 minutes.

Runtime.totalMemory()=2871001088

INFO 2022-08-25 10:10:39 AddOrReplaceReadGroups

********** NOTE: Picard's command line syntax is changing.

**********

********** For more information, please see:

**********

https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)

**********

********** The command line looks like this in the new syntax:

**********

********** AddOrReplaceReadGroups -I /ches/data10/lgspeight/results/Align/A_1_32.bam -O /ches/data10/lgspeight/results/Align/A_1_32.2.bam -RGID 4 -RGLB lib1 -RGPL ILLUMINA -RGPU unit1 -RGSM 20

**********

10:10:40.436 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/ches/home00/lgspeight/picard-2.27.4/picard/build/libs/picard.jar!/com/intel/gkl/native/libgkl_compression.so

[Thu Aug 25 10:10:40 EDT 2022] AddOrReplaceReadGroups INPUT=/ches/data10/lgspeight/results/Align/A_1_32.bam OUTPUT=/ches/data10/lgspeight/results/Align/A_1_32.2.bam RGID=4 RGLB=lib1 RGPL=ILLUMINA RGPU=unit1 RGSM=20 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false

[Thu Aug 25 10:10:40 EDT 2022] Executing as lgspeight@pm01.hpc.vims.edu on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_292-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.27.4-SNAPSHOT

INFO 2022-08-25 10:10:40 AddOrReplaceReadGroups Created read-group ID=4 PL=ILLUMINA LB=lib1 SM=20

INFO 2022-08-25 10:10:54 AddOrReplaceReadGroups Processed 1,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 13s. Last read position: NC_059305.1:61,973,973

INFO 2022-08-25 10:11:07 AddOrReplaceReadGroups Processed 2,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 12s. Last read position: NC_059306.1:34,228,113

INFO 2022-08-25 10:11:19 AddOrReplaceReadGroups Processed 3,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 12s. Last read position: NC_059306.1:89,574,840

INFO 2022-08-25 10:11:32 AddOrReplaceReadGroups Processed 4,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 12s. Last read position: NC_059307.1:17,365,946

INFO 2022-08-25 10:11:45 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 12s. Last read position: NC_059307.1:82,331,975

INFO 2022-08-25 10:11:58 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 12s. Last read position: NC_059308.1:41,536,741

INFO 2022-08-25 10:12:11 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 12s. Last read position: NC_059309.1:5,773,276

INFO 2022-08-25 10:12:24 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 12s. Last read position: NC_059309.1:60,862,275

INFO 2022-08-25 10:12:37 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 12s. Last read position: NC_059310.1:7,372,107

INFO 2022-08-25 10:12:49 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 12s. Last read position: NC_059310.1:59,160,424

INFO 2022-08-25 10:13:02 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 12s. Last read position: NC_059311.1:9,873,652

INFO 2022-08-25 10:13:14 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 12s. Last read position: NC_059311.1:51,585,895

INFO 2022-08-25 10:13:27 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 12s. Last read position: NC_059311.1:89,128,595

INFO 2022-08-25 10:13:40 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 12s. Last read position: NC_059312.1:35,981,845

INFO 2022-08-25 10:13:52 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 12s. Last read position: NC_059312.1:75,200,341

INFO 2022-08-25 10:14:05 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 12s. Last read position: NC_059313.1:27,201,631

INFO 2022-08-25 10:14:18 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 12s. Last read position: NC_059313.1:66,446,868

INFO 2022-08-25 10:14:30 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 12s. Last read position: NC_059313.1:103,510,691

INFO 2022-08-25 10:14:43 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 12s. Last read position: NC_059314.1:32,977,840

INFO 2022-08-25 10:14:56 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 12s. Last read position: NC_059314.1:83,398,361

INFO 2022-08-25 10:15:08 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 12s. Last read position: NC_059315.1:28,980,159

INFO 2022-08-25 10:15:21 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 12s. Last read position: NC_059315.1:72,355,237

INFO 2022-08-25 10:15:34 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 12s. Last read position: NC_059316.1:30,927,882

INFO 2022-08-25 10:15:47 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 12s. Last read position: NC_059317.1:6,306,235

INFO 2022-08-25 10:16:00 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 12s. Last read position: NC_059317.1:46,365,018

INFO 2022-08-25 10:16:12 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 12s. Last read position: NC_059317.1:70,743,720

INFO 2022-08-25 10:16:25 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 12s. Last read position: NC_059318.1:50,002,114

INFO 2022-08-25 10:16:37 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 12s. Last read position: NC_059318.1:87,467,719

INFO 2022-08-25 10:16:50 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 12s. Last read position: NC_059319.1:49,856,896

INFO 2022-08-25 10:17:03 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 12s. Last read position: NC_059320.1:15,994,957

INFO 2022-08-25 10:17:16 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 13s. Last read position: NC_059320.1:71,486,484

INFO 2022-08-25 10:17:28 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 12s. Last read position: NC_059321.1:37,235,293

INFO 2022-08-25 10:17:39 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 11s. Last read position: NC_059321.1:37,239,861

INFO 2022-08-25 10:17:51 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 11s. Last read position: NC_059321.1:37,252,878

INFO 2022-08-25 10:18:03 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 11s. Last read position: NC_059321.1:63,259,580

INFO 2022-08-25 10:18:16 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 12s. Last read position: NC_059322.1:41,562,729

INFO 2022-08-25 10:18:28 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 12s. Last read position: NC_059323.1:17,851,723

INFO 2022-08-25 10:18:41 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 12s. Last read position: NC_048487.1:4,074

INFO 2022-08-25 10:18:53 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 12s. Last read position: NC_048487.1:7,944

INFO 2022-08-25 10:19:05 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 12s. Last read position: */*

INFO 2022-08-25 10:19:18 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 12s. Last read position: */*

INFO 2022-08-25 10:19:31 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 12s. Last read position: */*

INFO 2022-08-25 10:19:44 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 12s. Last read position: */*

INFO 2022-08-25 10:19:57 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 13s. Last read position: */*

INFO 2022-08-25 10:20:10 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 13s. Last read position: */*

INFO 2022-08-25 10:20:23 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 13s. Last read position: */*

[Thu Aug 25 10:20:27 EDT 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 9.79 minutes.

Runtime.totalMemory()=1512570880

Using GATK jar /ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar

Running:

java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar ASEReadCounter -R /ches/data10/lgspeight/RNA-Seq/01_rawdata/genome/Clam_genome.fna -I /ches/data10/lgspeight/results/Align/A_1_32.2.bam -V /ches/data10/lgspeight/results/SNP_Call/SNPS/A_1_32-var.final.vcf.gz -O /ches/data10/lgspeight/results/ASE/A_1_32.table

10:20:31.049 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/ches/home00/lgspeight/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so

10:20:31.259 INFO ASEReadCounter - ------------------------------------------------------------

10:20:31.260 INFO ASEReadCounter - The Genome Analysis Toolkit (GATK) v4.2.6.1

10:20:31.261 INFO ASEReadCounter - For support and documentation go to https://software.broadinstitute.org/gatk/

10:20:31.261 INFO ASEReadCounter - Executing as lgspeight@pm01.hpc.vims.edu on Linux v3.10.0-514.el7.x86_64 amd64

10:20:31.262 INFO ASEReadCounter - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_292-b10

10:20:31.262 INFO ASEReadCounter - Start Date/Time: August 25, 2022 10:20:31 AM EDT

10:20:31.263 INFO ASEReadCounter - ------------------------------------------------------------

10:20:31.264 INFO ASEReadCounter - HTSJDK Version: 2.24.1

10:20:31.265 INFO ASEReadCounter - Picard Version: 2.27.1

10:20:31.265 INFO ASEReadCounter - Built for Spark Version: 2.4.5

10:20:31.265 INFO ASEReadCounter - HTSJDK Defaults.COMPRESSION_LEVEL : 2

10:20:31.266 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

10:20:31.266 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

10:20:31.266 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

10:20:31.267 INFO ASEReadCounter - Deflater: IntelDeflater

10:20:31.267 INFO ASEReadCounter - Inflater: IntelInflater

10:20:31.267 INFO ASEReadCounter - GCS max retries/reopens: 20

10:20:31.267 INFO ASEReadCounter - Requester pays: disabled

10:20:31.268 INFO ASEReadCounter - Initializing engine

10:20:32.349 INFO FeatureManager - Using codec VCFCodec to read file file:///ches/data10/lgspeight/results/SNP_Call/SNPS/A_1_32-var.final.vcf.gz

10:20:32.556 INFO ASEReadCounter - Done initializing engine

10:20:32.563 INFO ProgressMeter - Starting traversal

10:20:32.563 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute

10:20:32.694 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17635

10:20:32.703 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17649

10:20:32.704 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17652

10:20:32.715 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17693

10:20:32.721 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17738

10:20:32.724 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17780

10:20:32.726 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17795

10:20:32.730 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17823

10:20:32.731 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17824

10:20:32.731 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17825

10:20:32.738 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17848

10:20:32.747 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17960

10:20:32.747 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17961

10:20:32.748 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:17962

10:20:32.756 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:53708

10:20:32.757 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:53773

10:20:32.757 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:53774

10:20:32.757 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:53805

10:20:32.758 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:53833

10:20:32.758 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:53885

10:20:32.759 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:53910

10:20:32.759 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:53921

10:20:32.765 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:88233

10:20:32.765 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:88234

10:20:32.765 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:88235

10:20:32.765 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:88236

10:20:32.765 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:88237

10:20:32.765 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:88238

10:20:32.772 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:88594

10:20:32.776 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:89303

10:20:32.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:101686

10:20:32.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:101692

10:20:32.797 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:175603

10:20:32.798 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:175647

10:20:32.799 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:175710

10:20:32.799 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:175720

10:20:32.831 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:294250

10:20:32.844 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:302438

10:20:32.844 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:302473

10:20:32.844 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:302483

10:20:32.853 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:305782

10:20:32.865 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:307388

10:20:32.893 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:318624

10:20:32.894 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:318663

10:20:32.894 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:318709

10:20:32.896 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:319080

10:20:32.897 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:319189

10:20:32.901 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:320764

10:20:32.968 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:379966

10:20:32.969 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:380374

10:20:33.021 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:409110

10:20:33.037 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:418161

10:20:33.037 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:418177

10:20:33.038 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:418226

10:20:33.038 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:418267

10:20:33.075 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:439003

10:20:33.075 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:439028

10:20:33.076 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:439069

10:20:33.130 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:688150

10:20:33.131 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:737913

10:20:33.132 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:737949

10:20:33.132 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:737965

10:20:33.132 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:738016

10:20:33.133 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:738019

10:20:33.137 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:880879

10:20:33.137 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:880883

10:20:33.138 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:880965

10:20:33.138 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:880981

10:20:33.138 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:881011

10:20:33.191 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:972414

10:20:33.192 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:972723

10:20:33.221 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1075252

10:20:33.221 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1075253

10:20:33.221 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1075254

10:20:33.227 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1079125

10:20:33.228 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1079171

10:20:33.232 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1080550

10:20:33.257 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1107648

10:20:33.259 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1111312

10:20:33.260 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1111462

10:20:33.260 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1111475

10:20:33.262 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1115182

10:20:33.263 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1115299

10:20:33.264 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1115337

10:20:33.264 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1115346

10:20:33.286 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1128753

10:20:33.286 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1128825

10:20:33.286 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1128870

10:20:33.286 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1128885

10:20:33.288 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1129075

10:20:33.289 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1129215

10:20:33.289 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1129232

10:20:33.289 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1129323

10:20:33.290 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1129461

10:20:33.294 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1129876

10:20:33.296 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130129

10:20:33.297 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130229

10:20:33.299 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130371

10:20:33.299 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130414

10:20:33.300 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130415

10:20:33.300 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130416

10:20:33.300 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130417

10:20:33.300 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130418

10:20:33.301 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130419

10:20:33.301 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130420

10:20:33.305 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130654

10:20:33.305 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130664

10:20:33.307 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1130924

10:20:33.308 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131058

10:20:33.308 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131059

10:20:33.308 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131060

10:20:33.308 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131061

10:20:33.309 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131062

10:20:33.309 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131134

10:20:33.309 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131141

10:20:33.312 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131352

10:20:33.313 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1131390

10:20:33.320 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132144

10:20:33.320 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132166

10:20:33.321 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132331

10:20:33.322 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132384

10:20:33.323 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132496

10:20:33.326 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132535

10:20:33.327 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132565

10:20:33.327 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132626

10:20:33.327 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132632

10:20:33.328 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132644

10:20:33.328 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132647

10:20:33.329 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132748

10:20:33.329 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132769

10:20:33.330 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132840

10:20:33.330 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132841

10:20:33.330 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132842

10:20:33.330 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132864

10:20:33.332 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1132948

10:20:33.333 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133004

10:20:33.335 WARN ASEReadCounter - Ignoring site: cannot run ASE on non-biallelic sites: [VC Unknown @ NC_059305.1:1133075 Q192.71 of type=SNP alleles=[G*, A, T] attr={AC=[1, 1], AN=2, DP=17, DP4=[0, 0, 8, 9], FS=0, MQ=60, MQ0F=0, MQSBZ=0, SGB=-0.690438, VDB=0.0134843} GT=GT:PL 1/2:255,174,144,227,0,206 filters=

10:20:33.337 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133167

10:20:33.343 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133643

10:20:33.343 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133654

10:20:33.344 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133662

10:20:33.344 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133732

10:20:33.344 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133733

10:20:33.347 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133861

10:20:33.348 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133880

10:20:33.348 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1133917

10:20:33.350 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1134154

10:20:33.351 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1134155

10:20:33.353 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1134723

10:20:33.372 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1142318

10:20:33.372 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1142334

10:20:33.384 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1149057

10:20:33.401 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159542

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159543

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159544

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159545

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159546

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159547

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159548

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159549

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159550

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159551

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159552

10:20:33.402 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1159553

10:20:33.416 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1166830

10:20:33.416 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1166832

10:20:33.416 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1166876

10:20:33.416 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1166899

10:20:33.416 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1166900

10:20:33.448 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1184700

10:20:33.462 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1193261

10:20:33.463 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1193299

10:20:33.463 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1193320

10:20:33.463 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1193418

10:20:33.464 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1193419

10:20:33.471 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1197507

10:20:33.494 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1209456

10:20:33.496 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1209635

10:20:33.497 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1209869

10:20:33.497 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1209881

10:20:33.497 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1209897

10:20:33.497 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1209970

10:20:33.498 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1210021

10:20:33.498 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1210112

10:20:33.536 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1238784

10:20:33.536 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1238792

10:20:33.544 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1242931

10:20:33.548 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1246421

10:20:33.550 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1247865

10:20:33.565 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1259312

10:20:33.565 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1259408

10:20:33.567 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1260566

10:20:33.568 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1260626

10:20:33.568 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1260731

10:20:33.568 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1260820

10:20:33.588 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1282891

10:20:33.588 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1282892

10:20:33.588 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1282893

10:20:33.588 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1282894

10:20:33.588 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1282895

10:20:33.588 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1282896

10:20:33.588 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1282897

10:20:33.589 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1283441

10:20:33.590 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1283549

10:20:33.590 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1283729

10:20:33.590 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1283730

10:20:33.590 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1283731

10:20:33.598 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1294653

10:20:33.598 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1294654

10:20:33.598 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1294655

10:20:33.602 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1297407

10:20:33.602 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1297543

10:20:33.614 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1308658

10:20:33.620 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1314907

10:20:33.621 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1314947

10:20:33.621 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1315006

10:20:33.622 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1315248

10:20:33.622 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1315319

10:20:33.622 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1315386

10:20:33.622 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1315387

10:20:33.623 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1315388

10:20:33.625 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1317140

10:20:33.626 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1317918

10:20:33.627 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1318027

10:20:33.627 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1318028

10:20:33.627 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1318029

10:20:33.627 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1318030

10:20:33.627 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1318031

10:20:33.634 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1322084

10:20:33.634 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1322085

10:20:33.634 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1322086

10:20:33.634 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1322087

10:20:33.634 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1322088

10:20:33.635 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1322089

10:20:33.635 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1322238

10:20:33.643 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1327415

10:20:33.643 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1327477

10:20:33.644 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1327553

10:20:33.644 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1327567

10:20:33.645 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1327584

10:20:33.645 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1327598

10:20:33.660 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1337641

10:20:33.675 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1349108

10:20:33.675 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1349109

10:20:33.675 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1349110

10:20:33.675 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1349111

10:20:33.675 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1349112

10:20:33.700 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371000

10:20:33.700 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371019

10:20:33.700 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371021

10:20:33.700 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371142

10:20:33.700 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371143

10:20:33.701 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371144

10:20:33.701 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371145

10:20:33.701 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371146

10:20:33.701 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371147

10:20:33.701 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371148

10:20:33.701 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371167

10:20:33.702 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371467

10:20:33.702 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371489

10:20:33.702 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371548

10:20:33.703 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371558

10:20:33.703 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371602

10:20:33.704 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371622

10:20:33.705 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1371773

10:20:33.712 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1377277

10:20:33.712 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1377278

10:20:33.712 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1377304

10:20:33.713 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1377322

10:20:33.715 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1379021

10:20:33.715 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1379095

10:20:33.739 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1404569

10:20:33.740 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1404570

10:20:33.740 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1404571

10:20:33.740 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1404572

10:20:33.740 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1404573

10:20:33.740 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1404574

10:20:33.740 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1404575

10:20:33.740 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1404576

10:20:33.749 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1416464

10:20:33.772 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1445035

10:20:33.785 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1463588

10:20:33.785 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1463592

10:20:33.786 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1464450

10:20:33.786 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1464451

10:20:33.786 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1464452

10:20:33.786 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1464474

10:20:33.786 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1464582

10:20:33.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1466820

10:20:33.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1466856

10:20:33.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1466998

10:20:33.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1467015

10:20:33.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1467080

10:20:33.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1467084

10:20:33.790 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1467085

10:20:33.798 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1477802

10:20:33.798 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1477835

10:20:33.799 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1478043

10:20:33.799 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1478061

10:20:33.800 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1478309

10:20:33.800 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1478327

10:20:33.801 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1478345

10:20:33.801 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1478363

10:20:33.801 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1478397

10:20:33.803 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1478809

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479593

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479606

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479607

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479608

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479609

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479610

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479611

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479612

10:20:33.805 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479744

10:20:33.806 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1479771

10:20:33.807 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481505

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481577

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481605

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481606

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481607

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481608

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481609

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481610

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481611

10:20:33.808 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481612

10:20:33.809 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481613

10:20:33.809 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1481614

10:20:33.814 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1486738

10:20:33.814 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1486823

10:20:33.815 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1486946

10:20:33.818 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1491300

10:20:33.819 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1491323

10:20:33.819 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1491366

10:20:33.819 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1491367

10:20:33.819 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1491368

10:20:33.819 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1491369

10:20:33.819 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1491370

10:20:33.824 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1496285

10:20:33.825 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1496445

10:20:33.825 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1496462

10:20:33.828 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1497078

10:20:33.835 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1499249

10:20:33.836 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1499277

10:20:33.837 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1499627

10:20:33.839 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500025

10:20:33.840 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500148

10:20:33.840 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500218

10:20:33.841 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500308

10:20:33.841 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500318

10:20:33.841 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500359

10:20:33.841 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500360

10:20:33.842 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500361

10:20:33.844 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500655

10:20:33.845 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500844

10:20:33.845 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1500847

10:20:33.852 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1504634

10:20:33.859 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1511057

10:20:33.862 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1512728

10:20:33.862 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1512735

10:20:33.862 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1512745

10:20:33.870 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1524651

10:20:33.876 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1529642

10:20:33.877 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1529811

10:20:33.878 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1531000

10:20:33.909 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1555728

10:20:33.910 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1555992

10:20:33.914 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557410

10:20:33.914 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557614

10:20:33.914 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557615

10:20:33.914 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557616

10:20:33.914 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557617

10:20:33.914 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557618

10:20:33.914 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557619

10:20:33.915 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557620

10:20:33.915 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557621

10:20:33.915 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557622

10:20:33.915 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557623

10:20:33.915 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1557624

10:20:33.931 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1574784

10:20:33.932 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1574855

10:20:33.932 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1574911

10:20:33.934 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1576841

10:20:33.934 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1576842

10:20:33.935 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1576843

10:20:33.935 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1576844

10:20:33.937 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579679

10:20:33.938 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579882

10:20:33.938 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579883

10:20:33.938 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579884

10:20:33.938 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579885

10:20:33.938 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579886

10:20:33.938 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579887

10:20:33.938 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579888

10:20:33.938 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1579942

10:20:33.946 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1589158

10:20:33.946 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1589278

10:20:33.951 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1595590

10:20:33.954 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1617584

10:20:33.965 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1630285

10:20:33.965 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1630289

10:20:34.000 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1656168

10:20:34.010 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1656957

10:20:34.010 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1656958

10:20:34.010 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1656959

10:20:34.036 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1661938

10:20:34.039 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1662523

10:20:34.039 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1662524

10:20:34.043 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1663063

10:20:34.071 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1672551

10:20:34.082 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1678047

10:20:34.083 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1678220

10:20:34.083 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1678251

10:20:34.092 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1682194

10:20:34.092 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1682195

10:20:34.092 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1682232

10:20:34.092 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1682438

10:20:34.106 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1691441

10:20:34.106 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1691484

10:20:34.106 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1691485

10:20:34.107 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1691608

10:20:34.111 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1694219

10:20:34.112 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1694401

10:20:34.112 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1694537

10:20:34.113 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1694700

10:20:34.113 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1694749

10:20:34.113 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1694775

10:20:34.113 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1694786

10:20:34.113 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1694904

10:20:34.114 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695138

10:20:34.114 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695139

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695140

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695141

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695142

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695143

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695193

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695215

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695277

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695335

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695336

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695337

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695338

10:20:34.115 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695339

10:20:34.116 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1695340

10:20:34.132 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1706939

10:20:34.145 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1719275

10:20:34.145 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1719320

10:20:34.166 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1734784

10:20:34.174 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1758388

10:20:34.175 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1774396

10:20:34.175 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1774404

10:20:34.181 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1776046

10:20:34.182 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1776097

10:20:34.183 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1776162

10:20:34.190 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1776730

10:20:34.196 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1777190

10:20:34.197 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1777209

10:20:34.217 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1778349

10:20:34.222 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1778740

10:20:34.223 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1778804

10:20:34.224 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1778919

10:20:34.226 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1779035

10:20:34.226 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1779079

10:20:34.227 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1779150

10:20:34.300 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1788649

10:20:34.406 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1799377

10:20:34.416 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1802877

10:20:34.417 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1803175

10:20:34.473 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1933651

10:20:34.474 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1933913

10:20:34.474 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1933929

10:20:34.474 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1934026

10:20:34.484 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1945299

10:20:34.484 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1945308

10:20:34.484 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1945320

10:20:34.485 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1945385

10:20:34.492 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1954088

10:20:34.492 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1954120

10:20:34.492 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1954135

10:20:34.500 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1963657

10:20:34.500 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1963717

10:20:34.505 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1967924

10:20:34.509 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1970068

10:20:34.510 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1970289

10:20:34.511 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1970632

10:20:34.511 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1970633

10:20:34.511 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1970837

10:20:34.512 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:1970946

10:20:34.560 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2051148

10:20:34.562 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2096575

10:20:34.563 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2096878

10:20:34.568 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2099108

10:20:34.569 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2099391

10:20:34.570 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2099570

10:20:34.572 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2099929

10:20:34.572 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2100114

10:20:34.573 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2100973

10:20:34.575 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2103692

10:20:34.575 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2103693

10:20:34.575 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2103694

10:20:34.575 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2103695

10:20:34.575 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2103696

10:20:34.576 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2103821

10:20:34.579 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2109519

10:20:34.579 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2109520

10:20:34.579 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2109521

10:20:34.579 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2109522

10:20:34.580 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2110480

10:20:34.580 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2111528

10:20:34.580 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2111562

10:20:34.586 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2121400

10:20:34.586 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2121418

10:20:34.586 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2121444

10:20:34.586 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2121450

10:20:34.587 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2122609

10:20:34.587 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2122618

10:20:34.598 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2135877

10:20:34.654 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2336222

10:20:34.656 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2341758

10:20:34.656 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2341868

10:20:34.657 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2341896

10:20:34.657 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2341978

10:20:34.658 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342040

10:20:34.659 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342174

10:20:34.659 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342175

10:20:34.659 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342176

10:20:34.663 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342693

10:20:34.664 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342737

10:20:34.664 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342744

10:20:34.664 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342755

10:20:34.664 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342763

10:20:34.665 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2342813

10:20:34.667 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343039

10:20:34.667 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343066

10:20:34.667 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343083

10:20:34.667 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343100

10:20:34.667 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343122

10:20:34.668 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343191

10:20:34.669 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343288

10:20:34.669 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343326

10:20:34.669 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343327

10:20:34.669 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343348

10:20:34.669 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343368

10:20:34.669 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343523

10:20:34.670 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343538

10:20:34.670 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343545

10:20:34.670 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343627

10:20:34.670 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343653

10:20:34.670 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343665

10:20:34.670 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343674

10:20:34.670 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343679

10:20:34.670 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343689

10:20:34.671 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343777

10:20:34.671 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343810

10:20:34.671 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2343837

10:20:34.672 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344523

10:20:34.672 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344524

10:20:34.672 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344525

10:20:34.672 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344548

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344608

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344609

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344668

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344669

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344670

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344671

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344672

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344673

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344674

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344675

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344676

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344701

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344714

10:20:34.673 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344720

10:20:34.674 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2344799

10:20:34.676 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2345076

10:20:34.677 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2345205

10:20:34.677 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2345206

10:20:34.677 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2345207

10:20:34.677 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2345208

10:20:34.677 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2345209

10:20:34.677 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2345331

10:20:34.678 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2345532

10:20:34.680 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346130

10:20:34.680 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346131

10:20:34.680 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346132

10:20:34.680 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346133

10:20:34.680 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346134

10:20:34.681 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346135

10:20:34.681 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346150

10:20:34.681 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346151

10:20:34.681 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346225

10:20:34.682 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346700

10:20:34.682 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346709

10:20:34.683 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346746

10:20:34.683 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346775

10:20:34.683 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346799

10:20:34.683 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346890

10:20:34.683 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346891

10:20:34.683 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2346939

10:20:34.686 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2348089

10:20:34.686 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2348090

10:20:34.686 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2348095

10:20:34.686 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2348176

10:20:34.687 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2348408

10:20:34.687 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2348481

10:20:34.687 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2348488

10:20:34.690 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2349825

10:20:34.693 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2351043

10:20:34.702 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2356781

10:20:34.702 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2356782

10:20:34.702 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2356783

10:20:34.702 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2356784

10:20:34.710 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2362049

10:20:34.711 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2362448

10:20:34.713 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2364138

10:20:34.715 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2364629

10:20:34.719 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2367161

10:20:34.719 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2367170

10:20:34.719 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2367173

10:20:34.720 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2367176

10:20:34.720 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2367189

10:20:34.732 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2375915

10:20:34.732 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2375941

10:20:34.732 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2375942

10:20:34.733 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2376261

10:20:34.733 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2376269

10:20:34.733 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2376329

10:20:34.736 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2377459

10:20:34.739 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2378384

10:20:34.739 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2378453

10:20:34.741 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2379403

10:20:34.742 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2379872

10:20:34.756 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2389163

10:20:34.756 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2389519

10:20:34.758 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2389820

10:20:34.758 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2389826

10:20:34.758 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2389853

10:20:34.758 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2389867

10:20:34.761 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2390982

10:20:34.772 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2402155

10:20:34.779 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2403747

10:20:34.780 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2403955

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405540

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405569

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405570

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405641

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405642

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405643

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405644

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405645

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405646

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405647

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405870

10:20:34.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2405907

10:20:34.785 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2406138

10:20:34.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2407857

10:20:34.792 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2409314

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410007

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410008

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410009

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410010

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410011

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410012

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410013

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410025

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410158

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410254

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410255

10:20:34.793 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410286

10:20:34.794 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2410614

10:20:34.798 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2416505

10:20:34.826 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2462559

10:20:34.826 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2462587

10:20:34.826 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2462623

10:20:34.837 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2512904

10:20:34.837 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2512932

10:20:34.837 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2515769

10:20:34.839 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2517733

10:20:34.845 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2525506

10:20:34.846 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2525554

10:20:34.846 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2525665

10:20:34.846 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2526038

10:20:34.846 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2526074

10:20:34.846 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2526089

10:20:34.846 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2526213

10:20:34.846 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2526219

10:20:34.846 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2526333

10:20:34.847 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2526886

10:20:34.847 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2526925

10:20:34.847 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2527642

10:20:34.847 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2527657

10:20:34.847 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2527659

10:20:34.847 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2527706

10:20:34.848 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2533287

10:20:34.857 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2534581

10:20:34.874 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2534982

10:20:34.886 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2535320

10:20:34.987 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2539935

10:20:35.024 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2542130

10:20:35.024 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2542132

10:20:35.024 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2542133

10:20:35.030 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2544469

10:20:35.030 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2544490

10:20:35.031 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2571628

10:20:35.031 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2571629

10:20:35.031 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2571630

10:20:35.031 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2571631

10:20:35.031 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2571632

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2571633

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576115

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576116

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576117

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576118

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576119

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576120

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576121

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576122

10:20:35.032 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2576123

10:20:38.483 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2662286

10:20:38.508 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2662398

10:20:38.522 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2662466

10:20:39.383 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2666549

10:20:43.257 INFO ProgressMeter - NC_059305.1:2682358 0.2 238000 1335453.1

10:20:43.722 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700027

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700101

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700102

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700103

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700104

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700105

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700106

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700107

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700108

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700109

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700139

10:20:43.723 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700236

10:20:43.724 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700267

10:20:43.724 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700306

10:20:43.725 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700389

10:20:43.725 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700398

10:20:43.725 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2700482

10:20:43.744 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2709917

10:20:43.779 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2723346

10:20:43.784 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2725521

10:20:43.785 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2725608

10:20:43.788 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2725953

10:20:43.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2726068

10:20:43.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2726255

10:20:43.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2726341

10:20:43.789 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2726430

10:20:43.790 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2726447

10:20:43.791 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2727556

10:20:43.791 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2727578

10:20:43.791 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2727611

10:20:43.791 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2727690

10:20:43.791 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2727720

10:20:43.791 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2727776

10:20:43.791 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2727779

10:20:43.795 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2733001

10:20:43.795 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2733008

10:20:43.795 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2733011

10:20:43.796 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2733138

10:20:43.803 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2734578

10:20:43.912 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2759043

10:20:43.933 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2768045

10:20:43.933 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2768046

10:20:43.933 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2768047

10:20:43.942 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2770218

10:20:43.942 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2770299

10:20:43.953 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2772553

10:20:43.960 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2775405

10:20:43.960 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2775412

10:20:43.963 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2780686

10:20:43.964 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2780773

10:20:43.965 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2781402

10:20:43.965 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2781495

10:20:43.965 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2781546

10:20:43.967 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2782911

10:20:43.967 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2782920

10:20:43.967 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2782944

10:20:43.967 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2782983

10:20:43.967 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2783007

10:20:43.968 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2783604

10:20:43.968 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2783699

10:20:43.968 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2783726

10:20:43.971 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2784990

10:20:43.975 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2788342

10:20:43.975 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2788366

10:20:43.975 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2788450

10:20:43.975 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2788451

10:20:43.975 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2788452

10:20:43.981 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2793671

10:20:43.981 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2793711

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2793840

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2793842

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2793864

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2793895

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2793908

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794038

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794075

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794079

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794110

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794165

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794192

10:20:43.982 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794197

10:20:43.983 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794220

10:20:43.983 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794262

10:20:43.984 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794674

10:20:43.984 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794675

10:20:43.984 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794676

10:20:43.984 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794677

10:20:43.984 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794678

10:20:43.984 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794679

10:20:43.984 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794680

10:20:43.984 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2794691

10:20:43.986 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795029

10:20:43.990 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795381

10:20:43.991 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795521

10:20:43.991 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795522

10:20:43.991 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795563

10:20:43.991 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795773

10:20:43.991 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795789

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795905

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795906

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795907

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795908

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795909

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795910

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795911

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795912

10:20:43.992 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2795967

10:20:43.994 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2796831

10:20:43.994 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2796832

10:20:43.994 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2796833

10:20:43.994 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2796834

10:20:43.995 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2796979

10:20:43.996 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2818275

10:20:44.001 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2821619

10:20:44.001 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2821643

10:20:44.001 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2821644

10:20:44.001 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2821652

10:20:44.017 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2840611

10:20:44.017 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2840654

10:20:44.017 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2840679

10:20:44.017 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2840698

10:20:44.017 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2840739

10:20:44.017 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2840746

10:20:44.017 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2840841

10:20:44.017 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2840844

10:20:44.044 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2870240

10:20:44.044 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2870300

10:20:44.051 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2878153

10:20:44.056 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2881566

10:20:44.056 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2881571

10:20:44.056 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2881600

10:20:44.056 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2881727

10:20:44.073 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2901122

10:20:44.074 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2902004

10:20:44.075 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2902739

10:20:44.076 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903194

10:20:44.076 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903200

10:20:44.076 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903201

10:20:44.076 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903202

10:20:44.076 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903375

10:20:44.076 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903436

10:20:44.076 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903495

10:20:44.077 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903665

10:20:44.077 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903716

10:20:44.078 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2903910

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904244

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904375

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904401

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904506

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904507

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904508

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904509

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904525

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904636

10:20:44.079 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904642

10:20:44.080 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904687

10:20:44.080 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904891

10:20:44.081 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904948

10:20:44.081 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2904955

10:20:44.081 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2905674

10:20:44.082 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2905826

10:20:44.082 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2905827

10:20:44.082 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2905835

10:20:44.082 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2905843

10:20:44.082 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2905846

10:20:44.082 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2905993

10:20:44.082 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2906114

10:20:44.083 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2906233

10:20:44.083 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2906283

10:20:44.083 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2906316

10:20:44.083 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2906368

10:20:44.083 WARN ASEReadCounter - Ignoring site: variant is not het at postion: NC_059305.1:2906369

10:20:44.086 INFO ASEReadCounter - Shutting down engine

[August 25, 2022 10:20:44 AM EDT] org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter done. Elapsed time: 0.22 minutes.

Runtime.totalMemory()=2632450048

***********************************************************************

A USER ERROR has occurred: More then one variant context at position: NC_059305.1:2906370

***********************************************************************

org.broadinstitute.hellbender.exceptions.UserException: More then one variant context at position: NC_059305.1:2906370

at org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter.apply(ASEReadCounter.java:193)

at org.broadinstitute.hellbender.engine.LocusWalker.lambda$traverse$0(LocusWalker.java:154)

at java.util.Iterator.forEachRemaining(Iterator.java:116)

at org.broadinstitute.hellbender.engine.LocusWalker.traverse(LocusWalker.java:152)

at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1085)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

at org.broadinstitute.hellbender.Main.main(Main.java:289)

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ASEReadCount Only Outputting the First Chromosome

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