ASEReadCounter outputting blank table
Answered
UPDATED: When I run ASEReadCounter, it outputs blank table. I have tried adding AddOrReplaceReadGroups to my job based on other posts, but this did not work. Do you think it is my VCF file? What do I need to change?
a) GATK version used: gatk-4.2.6.1
________________
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}.bam \
-V $VCFDIR/$SAMPLE-var.final.vcf.gz \
-O $WORKDIR/${SAMPLE}.table
_______________________________
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 2022-08-24 13:36:13 CreateSequenceDictionary Output dictionary will be written in /ches/data10/lgspeight/RNA-Seq/01_rawdata/genome/Clam_genome.dict
13:36:13.463 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
[Wed Aug 24 13:36:13 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
[Wed Aug 24 13:36:13 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
[Wed Aug 24 13:36:13 EDT 2022] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=2202533888
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
13:36:16.851 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
13:36:17.053 INFO IndexFeatureFile - ------------------------------------------------------------
13:36:17.054 INFO IndexFeatureFile - The Genome Analysis Toolkit (GATK) v4.2.6.1
13:36:17.054 INFO IndexFeatureFile - For support and documentation go to https://software.broadinstitute.org/gatk/
13:36:17.055 INFO IndexFeatureFile - Executing as lgspeight@pm01.hpc.vims.edu on Linux v3.10.0-514.el7.x86_64 amd64
13:36:17.055 INFO IndexFeatureFile - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_292-b10
13:36:17.056 INFO IndexFeatureFile - Start Date/Time: August 24, 2022 1:36:16 PM EDT
13:36:17.057 INFO IndexFeatureFile - ------------------------------------------------------------
13:36:17.057 INFO IndexFeatureFile - ------------------------------------------------------------
13:36:17.058 INFO IndexFeatureFile - HTSJDK Version: 2.24.1
13:36:17.059 INFO IndexFeatureFile - Picard Version: 2.27.1
13:36:17.059 INFO IndexFeatureFile - Built for Spark Version: 2.4.5
13:36:17.059 INFO IndexFeatureFile - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:36:17.060 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:36:17.060 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:36:17.060 INFO IndexFeatureFile - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:36:17.061 INFO IndexFeatureFile - Deflater: IntelDeflater
13:36:17.061 INFO IndexFeatureFile - Inflater: IntelInflater
13:36:17.061 INFO IndexFeatureFile - GCS max retries/reopens: 20
13:36:17.061 INFO IndexFeatureFile - Requester pays: disabled
13:36:17.062 INFO IndexFeatureFile - Initializing engine
13:36:17.062 INFO IndexFeatureFile - Done initializing engine
13:36:17.603 INFO FeatureManager - Using codec VCFCodec to read file file:///ches/data10/lgspeight/results/SNP_Call/SNPS/A_1_32-var.final.vcf.gz
13:36:17.704 INFO ProgressMeter - Starting traversal
13:36:17.705 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
13:36:23.055 WARN IntelInflater - Zero Bytes Written : 0
13:36:23.057 INFO ProgressMeter - NW_025543028.1:13539 0.1 755807 8476340.2
13:36:23.058 INFO ProgressMeter - Traversal complete. Processed 755807 total records in 0.1 minutes.
13:36:23.143 INFO IndexFeatureFile - Successfully wrote index to /ches/data10/lgspeight/results/SNP_Call/SNPS/A_1_32-var.final.vcf.gz.tbi
13:36:23.144 INFO IndexFeatureFile - Shutting down engine
[August 24, 2022 1:36:23 PM EDT] org.broadinstitute.hellbender.tools.IndexFeatureFile done. Elapsed time: 0.11 minutes.
Runtime.totalMemory()=2816999424
INFO 2022-08-24 13:36:23 AddOrReplaceReadGroups
********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
**********
**********
********** 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
**********
13:36:24.396 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
[Wed Aug 24 13:36:24 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
[Wed Aug 24 13:36:24 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 2022-08-24 13:36:24 AddOrReplaceReadGroups Created read-group ID=4 PL=ILLUMINA LB=lib1 SM=20
INFO 2022-08-24 13:36:38 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 2022-08-24 13:36:50 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 2022-08-24 13:37:03 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 2022-08-24 13:37:16 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 2022-08-24 13:37:28 AddOrReplaceReadGroups Processed 5,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 12s. Last read position: NC_059307.1:82,331,975
INFO 2022-08-24 13:37:41 AddOrReplaceReadGroups Processed 6,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 12s. Last read position: NC_059308.1:41,536,741
INFO 2022-08-24 13:37:54 AddOrReplaceReadGroups Processed 7,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 12s. Last read position: NC_059309.1:5,773,276
INFO 2022-08-24 13:38:06 AddOrReplaceReadGroups Processed 8,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 12s. Last read position: NC_059309.1:60,862,275
INFO 2022-08-24 13:38:19 AddOrReplaceReadGroups Processed 9,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 12s. Last read position: NC_059310.1:7,372,107
INFO 2022-08-24 13:38:31 AddOrReplaceReadGroups Processed 10,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 12s. Last read position: NC_059310.1:59,160,424
INFO 2022-08-24 13:38:44 AddOrReplaceReadGroups Processed 11,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 12s. Last read position: NC_059311.1:9,873,652
INFO 2022-08-24 13:38:56 AddOrReplaceReadGroups Processed 12,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 12s. Last read position: NC_059311.1:51,585,895
INFO 2022-08-24 13:39:08 AddOrReplaceReadGroups Processed 13,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 12s. Last read position: NC_059311.1:89,128,595
INFO 2022-08-24 13:39:21 AddOrReplaceReadGroups Processed 14,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 12s. Last read position: NC_059312.1:35,981,845
INFO 2022-08-24 13:39:33 AddOrReplaceReadGroups Processed 15,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 12s. Last read position: NC_059312.1:75,200,341
INFO 2022-08-24 13:39:46 AddOrReplaceReadGroups Processed 16,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 12s. Last read position: NC_059313.1:27,201,631
INFO 2022-08-24 13:39:58 AddOrReplaceReadGroups Processed 17,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 12s. Last read position: NC_059313.1:66,446,868
INFO 2022-08-24 13:40:11 AddOrReplaceReadGroups Processed 18,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 12s. Last read position: NC_059313.1:103,510,691
INFO 2022-08-24 13:40:23 AddOrReplaceReadGroups Processed 19,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 12s. Last read position: NC_059314.1:32,977,840
INFO 2022-08-24 13:40:36 AddOrReplaceReadGroups Processed 20,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 12s. Last read position: NC_059314.1:83,398,361
INFO 2022-08-24 13:40:49 AddOrReplaceReadGroups Processed 21,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 12s. Last read position: NC_059315.1:28,980,159
INFO 2022-08-24 13:41:01 AddOrReplaceReadGroups Processed 22,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 12s. Last read position: NC_059315.1:72,355,237
INFO 2022-08-24 13:41:14 AddOrReplaceReadGroups Processed 23,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 12s. Last read position: NC_059316.1:30,927,882
INFO 2022-08-24 13:41:26 AddOrReplaceReadGroups Processed 24,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 12s. Last read position: NC_059317.1:6,306,235
INFO 2022-08-24 13:41:39 AddOrReplaceReadGroups Processed 25,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 12s. Last read position: NC_059317.1:46,365,018
INFO 2022-08-24 13:41:51 AddOrReplaceReadGroups Processed 26,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 12s. Last read position: NC_059317.1:70,743,720
INFO 2022-08-24 13:42:04 AddOrReplaceReadGroups Processed 27,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 12s. Last read position: NC_059318.1:50,002,114
INFO 2022-08-24 13:42:16 AddOrReplaceReadGroups Processed 28,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 12s. Last read position: NC_059318.1:87,467,719
INFO 2022-08-24 13:42:29 AddOrReplaceReadGroups Processed 29,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 12s. Last read position: NC_059319.1:49,856,896
INFO 2022-08-24 13:42:41 AddOrReplaceReadGroups Processed 30,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 12s. Last read position: NC_059320.1:15,994,957
INFO 2022-08-24 13:42:54 AddOrReplaceReadGroups Processed 31,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 12s. Last read position: NC_059320.1:71,486,484
INFO 2022-08-24 13:43:06 AddOrReplaceReadGroups Processed 32,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 12s. Last read position: NC_059321.1:37,235,293
INFO 2022-08-24 13:43:18 AddOrReplaceReadGroups Processed 33,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 11s. Last read position: NC_059321.1:37,239,861
INFO 2022-08-24 13:43:29 AddOrReplaceReadGroups Processed 34,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 11s. Last read position: NC_059321.1:37,252,878
INFO 2022-08-24 13:43:41 AddOrReplaceReadGroups Processed 35,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 11s. Last read position: NC_059321.1:63,259,580
INFO 2022-08-24 13:43:53 AddOrReplaceReadGroups Processed 36,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 12s. Last read position: NC_059322.1:41,562,729
INFO 2022-08-24 13:44:06 AddOrReplaceReadGroups Processed 37,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 12s. Last read position: NC_059323.1:17,851,723
INFO 2022-08-24 13:44:18 AddOrReplaceReadGroups Processed 38,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 12s. Last read position: NC_048487.1:4,074
INFO 2022-08-24 13:44:30 AddOrReplaceReadGroups Processed 39,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 11s. Last read position: NC_048487.1:7,944
INFO 2022-08-24 13:44:42 AddOrReplaceReadGroups Processed 40,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 12s. Last read position: */*
INFO 2022-08-24 13:44:55 AddOrReplaceReadGroups Processed 41,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 12s. Last read position: */*
INFO 2022-08-24 13:45:08 AddOrReplaceReadGroups Processed 42,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 12s. Last read position: */*
INFO 2022-08-24 13:45:21 AddOrReplaceReadGroups Processed 43,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 12s. Last read position: */*
INFO 2022-08-24 13:45:33 AddOrReplaceReadGroups Processed 44,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 12s. Last read position: */*
INFO 2022-08-24 13:45:46 AddOrReplaceReadGroups Processed 45,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 12s. Last read position: */*
INFO 2022-08-24 13:45:59 AddOrReplaceReadGroups Processed 46,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 12s. Last read position: */*
[Wed Aug 24 13:46:03 EDT 2022] picard.sam.AddOrReplaceReadGroups done. Elapsed time: 9.66 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.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
13:46:07.076 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
13:46:07.283 INFO ASEReadCounter - ------------------------------------------------------------
13:46:07.284 INFO ASEReadCounter - The Genome Analysis Toolkit (GATK) v4.2.6.1
13:46:07.284 INFO ASEReadCounter - For support and documentation go to https://software.broadinstitute.org/gatk/
13:46:07.284 INFO ASEReadCounter - Executing as lgspeight@pm01.hpc.vims.edu on Linux v3.10.0-514.el7.x86_64 amd64
13:46:07.285 INFO ASEReadCounter - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_292-b10
13:46:07.286 INFO ASEReadCounter - Start Date/Time: August 24, 2022 1:46:07 PM EDT
13:46:07.286 INFO ASEReadCounter - ------------------------------------------------------------
13:46:07.286 INFO ASEReadCounter - ------------------------------------------------------------
13:46:07.287 INFO ASEReadCounter - HTSJDK Version: 2.24.1
13:46:07.288 INFO ASEReadCounter - Picard Version: 2.27.1
13:46:07.288 INFO ASEReadCounter - Built for Spark Version: 2.4.5
13:46:07.288 INFO ASEReadCounter - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:46:07.289 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:46:07.289 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:46:07.289 INFO ASEReadCounter - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:46:07.289 INFO ASEReadCounter - Deflater: IntelDeflater
13:46:07.290 INFO ASEReadCounter - Inflater: IntelInflater
13:46:07.290 INFO ASEReadCounter - GCS max retries/reopens: 20
13:46:07.290 INFO ASEReadCounter - Requester pays: disabled
13:46:07.291 INFO ASEReadCounter - Initializing engine
13:46:08.125 INFO FeatureManager - Using codec VCFCodec to read file file:///ches/data10/lgspeight/results/SNP_Call/SNPS/A_1_32-var.final.vcf.gz
13:46:08.300 INFO ASEReadCounter - Done initializing engine
13:46:08.304 INFO ProgressMeter - Starting traversal
13:46:08.304 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
13:47:34.105 WARN IntelInflater - Zero Bytes Written : 0
13:47:34.111 INFO ASEReadCounter - 0 read(s) filtered by: ValidAlignmentStartReadFilter
0 read(s) filtered by: ValidAlignmentEndReadFilter
46289917 read(s) filtered by: HasReadGroupReadFilter
0 read(s) filtered by: MatchingBasesAndQualsReadFilter
0 read(s) filtered by: SeqIsStoredReadFilter
0 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: NotSecondaryAlignmentReadFilter
0 read(s) filtered by: MappedReadFilter
46289917 total reads filtered
13:47:34.113 INFO ProgressMeter - unmapped 1.4 0 0.0
13:47:34.113 INFO ProgressMeter - Traversal complete. Processed 0 total loci in 1.4 minutes.
13:47:34.114 INFO ASEReadCounter - Shutting down engine
[August 24, 2022 1:47:34 PM EDT] org.broadinstitute.hellbender.tools.walkers.rnaseq.ASEReadCounter done. Elapsed time: 1.45 minutes.
Runtime.totalMemory()=3546808320
-
Hi Leslie Youtsey,
Thank you for writing to the GATK forum. I hope that we can help you sort this out.
Our developers noticed that ASEReadCounter likely failed because the BAM does not specify a read group. You populated the read groups with AddOrReplaceReadGroups before proceeding to count them. You seem to be using the original BAM as input to ASEReaderCounter, rather than the newly generated BAM with the read groups.
In the final step, the input BAM should be:
/ches/data10/lgspeight/results/Align/A_1_32.2.bam
not,
/ches/data10/lgspeight/results/Align/A_1_32.bam
Please let me know if this helps! Feel free to reach out with any further questions.
Best,
Anthony -
That did the trick! Thanks Anthony DiCi. Sometimes it just takes a second eye to catch the small things.
The table output looks good! But I have a second questions. In the table is the contig and position of the SNP, but I would like to add the gene or feature that the SNP is within. This would involve the gff annotation file. Do you know of a tool that GATK offers that could add this to the table?
-
Hi Leslie Youtsey,
Thank you so much for following up! Yes, sometimes all we need is an extra set of eyes in these circumstances.
Regarding your inquiry about any GATK tools that would allow you to annotate your output table, we do!
Funcotator is a functional annotation tool that allows users to add annotations to called variants based on a set of data sources, each with its own matching criteria. Please find the tool index for Funcotator here. There are a variety of Funcotator-specific arguments allowing you to customize your annotations within the index.
I hope this helps! Please let me know if you find success with this tool. If you have any other questions as you go along, please don’t hesitate to reach back out.
Best,
Anthony -
Hi Leslie Youtsey,
We haven’t heard from you in a while so we will be closing out your ticket in our system. If you still require assistance, you need only respond to this thread, and we’ll make you a follow-up ticket to pick up where we left off.
Thank you again for contributing to our GATK forum!
Best,
Anthony
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