• GATK version:  v4.2.3.0
• Command used:  I ran HaplotypeCaller in both GVCF mode and single sample mode.

gatk --java-options "-Xmx30g" HaplotypeCaller  \
-R Homo_sapiens_assembly19.fasta  \
-I SRR8788980.1.bam  \
-O output.g.vcf.gz \
-ERC GVCF


gatk --java-options "-Xmx30g" HaplotypeCaller  \
   -R Homo_sapiens_assembly19.fasta \
   -I  SRR8788980.1.bam \
   -O  SRR8788980.1.output.g.vcf.gz

• Problem:  Both VCF and GVCF output files only contain uninformative records 

GVCF mode:

VCF mode(nothing output):

• Files contained in the directory where the command was run: 

Single sample name: SRR8788980.1 (I used command samtools index xxx.bam to generate SRR8788980.1.bai )

Reference: Homo_sapiens_assembly19.fasta  (I used picard and samtools to generate Homo_sapiens_assembly19.dict and Homo_sapiens_assembly19.fasta.fai index files)

• Standard output of GVCF model:

Using GATK jar /home/lzhexin/softwares/gatk-4.2.3.0/gatk-package-4.2.3.0-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 -Xmx30g -jar /home/lzhexin/softwares/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar HaplotypeCaller -R Homo_sapiens_assembly19.fasta -I SRR8788980.1.bam -O /scratch/output_dir_haplotypecaller_single/SRR8788980.1.output.g.vcf.gz

15:20:28.937 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/lzhexin/softwares/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

Dec 07, 2021 3:20:29 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

INFO: Failed to detect whether we are running on Google Compute Engine.

15:20:29.150 INFO HaplotypeCaller - ------------------------------------------------------------

15:20:29.151 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.2.3.0

15:20:29.151 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/

15:20:29.151 INFO HaplotypeCaller - Executing as lzhexin@r31n3.lisa.surfsara.nl on Linux v4.19.0-18-amd64 amd64

15:20:29.151 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v11.0.12+7-post-Debian-2deb10u1

15:20:29.152 INFO HaplotypeCaller - Start Date/Time: December 7, 2021 at 3:20:28 PM CET

15:20:29.152 INFO HaplotypeCaller - ------------------------------------------------------------

15:20:29.152 INFO HaplotypeCaller - ------------------------------------------------------------

15:20:29.153 INFO HaplotypeCaller - HTSJDK Version: 2.24.1

15:20:29.153 INFO HaplotypeCaller - Picard Version: 2.25.4

15:20:29.153 INFO HaplotypeCaller - Built for Spark Version: 2.4.5

15:20:29.153 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2

15:20:29.153 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

15:20:29.153 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

15:20:29.153 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

15:20:29.154 INFO HaplotypeCaller - Deflater: IntelDeflater

15:20:29.154 INFO HaplotypeCaller - Inflater: IntelInflater

15:20:29.154 INFO HaplotypeCaller - GCS max retries/reopens: 20

15:20:29.154 INFO HaplotypeCaller - Requester pays: disabled

15:20:29.154 INFO HaplotypeCaller - Initializing engine

WARNING: BAM index file /scratch/one_sample/SRR8788980.1.bam.bai is older than BAM /scratch/one_sample/SRR8788980.1.bam

15:20:29.407 INFO HaplotypeCaller - Done initializing engine

15:20:29.419 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output

15:20:29.436 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/lzhexin/softwares/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_utils.so

15:20:29.639 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/lzhexin/softwares/gatk-4.2.3.0/gatk-package-4.2.3.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so

15:20:29.685 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions

15:20:29.685 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM

15:20:29.686 INFO IntelPairHmm - Available threads: 4

15:20:29.686 INFO IntelPairHmm - Requested threads: 4

15:20:29.686 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation

15:20:29.720 INFO ProgressMeter - Starting traversal

15:20:29.720 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute

15:20:39.721 INFO ProgressMeter - 1:33404701 0.2 111350 668100.0

15:20:49.721 INFO ProgressMeter - 1:69209701 0.3 230700 692100.0

15:20:59.721 INFO ProgressMeter - 1:105281701 0.5 350940 701880.0

15:21:09.720 INFO ProgressMeter - 1:141350701 0.7 471170 706755.0

15:21:19.720 INFO ProgressMeter - 1:177320701 0.8 591070 709284.0

15:21:29.721 INFO ProgressMeter - 1:213317701 1.0 711060 711060.0

15:21:39.721 INFO ProgressMeter - 2:24901 1.2 830920 712207.0

15:21:49.721 INFO ProgressMeter - 2:37335901 1.3 955290 716458.5

15:21:59.721 INFO ProgressMeter - 2:75102901 1.5 1081180 720778.7

15:22:09.722 INFO ProgressMeter - 2:112761901 1.7 1206710 724018.8

15:22:19.721 INFO ProgressMeter - 2:148767901 1.8 1326730 723664.3

15:22:29.721 INFO ProgressMeter - 2:183126901 2.0 1441260 720624.0

15:22:39.721 INFO ProgressMeter - 2:217518901 2.2 1555900 718102.2

15:22:49.721 INFO ProgressMeter - 3:9533401 2.3 1673280 717114.9

15:22:59.721 INFO ProgressMeter - 3:47219401 2.5 1798900 719555.2

15:23:09.721 INFO ProgressMeter - 3:84989401 2.7 1924800 721795.5

15:23:19.721 INFO ProgressMeter - 3:122636401 2.8 2050290 723627.5

15:23:29.721 INFO ProgressMeter - 3:157670401 3.0 2167070 722352.7

15:23:39.722 INFO ProgressMeter - 3:191960401 3.2 2281370 720428.8

15:23:49.721 INFO ProgressMeter - 4:31011901 3.3 2404950 721481.4

15:23:59.721 INFO ProgressMeter - 4:68718901 3.5 2530640 723036.6

15:24:09.721 INFO ProgressMeter - 4:106350901 3.7 2656080 724382.2

15:24:19.721 INFO ProgressMeter - 4:142962901 3.8 2778120 724723.8

15:24:29.721 INFO ProgressMeter - 4:177210901 4.0 2892280 723067.0

15:24:39.722 INFO ProgressMeter - 5:22308601 4.2 3013120 723145.9

15:24:49.721 INFO ProgressMeter - 5:59994601 4.3 3138740 724321.8

15:24:59.721 INFO ProgressMeter - 5:97740601 4.5 3264560 725455.1

15:25:09.721 INFO ProgressMeter - 5:135042601 4.7 3388900 726190.3

15:25:19.721 INFO ProgressMeter - 5:169332601 4.8 3503200 724797.5

15:25:29.721 INFO ProgressMeter - 6:24774301 5.0 3624390 724875.6

15:25:39.722 INFO ProgressMeter - 6:62418301 5.2 3749870 725778.9

15:25:49.722 INFO ProgressMeter - 6:100002301 5.3 3875150 726588.4

15:25:59.721 INFO ProgressMeter - 6:137088301 5.5 3998770 727046.9

15:26:09.721 INFO ProgressMeter - 7:245101 5.7 4113010 725823.2

15:26:19.721 INFO ProgressMeter - 7:37820101 5.8 4238260 726556.8

15:26:29.721 INFO ProgressMeter - 7:75407101 6.0 4363550 727256.3

15:26:39.721 INFO ProgressMeter - 7:113033101 6.2 4488970 727939.1

15:26:49.722 INFO ProgressMeter - 7:149132101 6.3 4609300 727782.3

15:26:59.721 INFO ProgressMeter - 8:26566201 6.5 4731210 727876.6

15:27:09.721 INFO ProgressMeter - 8:64198201 6.7 4856650 728495.7

15:27:19.721 INFO ProgressMeter - 8:101827201 6.8 4982080 729083.1

15:27:29.721 INFO ProgressMeter - 8:138592201 7.0 5104630 729231.1

15:27:39.721 INFO ProgressMeter - 9:29097901 7.2 5227530 729421.1

15:27:49.721 INFO ProgressMeter - 9:66663901 7.3 5352750 729918.8

15:27:59.721 INFO ProgressMeter - 9:104268901 7.5 5478100 730411.7

15:28:09.721 INFO ProgressMeter - 9:140898901 7.7 5600200 730459.3

15:28:19.721 INFO ProgressMeter - 10:37281301 7.8 5725520 730915.9

15:28:29.721 INFO ProgressMeter - 10:74928301 8.0 5851010 731374.7

15:28:39.721 INFO ProgressMeter - 10:112575301 8.2 5976500 731814.8

15:28:49.721 INFO ProgressMeter - 11:14729401 8.3 6102130 732254.1

15:28:59.722 INFO ProgressMeter - 11:52319401 8.5 6227430 732637.4

15:29:09.721 INFO ProgressMeter - 11:89930401 8.7 6352800 733014.0

15:29:19.721 INFO ProgressMeter - 11:127595401 8.8 6478350 733396.7

15:29:29.721 INFO ProgressMeter - 12:29824801 9.0 6602470 733606.4

15:29:39.721 INFO ProgressMeter - 12:67396801 9.2 6727710 733930.7

15:29:49.721 INFO ProgressMeter - 12:105028801 9.3 6853150 734264.8

15:29:59.722 INFO ProgressMeter - 13:8799901 9.5 6978560 734584.0

15:30:09.721 INFO ProgressMeter - 13:46392901 9.7 7103870 734881.8

15:30:19.721 INFO ProgressMeter - 13:84009901 9.8 7229260 735177.7

15:30:29.721 INFO ProgressMeter - 14:6441901 10.0 7354600 735458.8

15:30:39.721 INFO ProgressMeter - 14:44031901 10.2 7479900 735726.7

15:30:49.721 INFO ProgressMeter - 14:81672901 10.3 7605370 736002.4

15:30:59.722 INFO ProgressMeter - 15:11883301 10.5 7730570 736243.6

15:31:09.722 INFO ProgressMeter - 15:49422301 10.7 7855700 736470.7

15:31:19.722 INFO ProgressMeter - 15:87018301 10.8 7981020 736708.4

15:31:29.721 INFO ProgressMeter - 16:22076701 11.0 8106320 736937.1

15:31:39.721 INFO ProgressMeter - 16:59696701 11.2 8231720 737167.9

15:31:49.721 INFO ProgressMeter - 17:7015801 11.3 8357300 737407.7

15:31:59.721 INFO ProgressMeter - 17:44569801 11.5 8482480 737605.9

15:32:09.721 INFO ProgressMeter - 18:1087501 11.7 8608190 737843.8

15:32:19.721 INFO ProgressMeter - 18:38812501 11.8 8733940 738078.4

15:32:29.721 INFO ProgressMeter - 18:76501501 12.0 8859570 738296.5

15:32:39.721 INFO ProgressMeter - 19:36095101 12.2 8985140 738503.6

15:32:49.721 INFO ProgressMeter - 20:14670001 12.3 9110820 738714.1

15:32:59.721 INFO ProgressMeter - 20:52314001 12.5 9236300 738903.0

15:33:09.722 INFO ProgressMeter - 21:26884201 12.7 9361620 739074.3

15:33:19.721 INFO ProgressMeter - 22:16395301 12.8 9487090 739252.8

15:33:29.721 INFO ProgressMeter - X:2722501 13.0 9612530 739424.4

15:33:39.721 INFO ProgressMeter - X:40342501 13.2 9737930 739588.7

15:33:49.721 INFO ProgressMeter - X:77974501 13.3 9863370 739751.8

15:33:59.721 INFO ProgressMeter - X:115594501 13.5 9988770 739908.0

15:34:09.721 INFO ProgressMeter - X:151156501 13.7 10107310 739558.4

15:34:19.722 INFO ProgressMeter - Y:33130801 13.8 10231460 739622.7

15:34:28.422 INFO HaplotypeCaller - 0 read(s) filtered by: MappingQualityReadFilter

0 read(s) filtered by: MappingQualityAvailableReadFilter

0 read(s) filtered by: MappedReadFilter

0 read(s) filtered by: NotSecondaryAlignmentReadFilter

0 read(s) filtered by: NotDuplicateReadFilter

0 read(s) filtered by: PassesVendorQualityCheckReadFilter

0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter

0 read(s) filtered by: GoodCigarReadFilter

0 read(s) filtered by: WellformedReadFilter

0 total reads filtered

15:34:28.423 INFO ProgressMeter - NC_007605:171001 14.0 10339962 739710.9

15:34:28.424 INFO ProgressMeter - Traversal complete. Processed 10339962 total regions in 14.0 minutes.

15:34:28.432 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0

15:34:28.432 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0

15:34:28.433 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec

15:34:28.434 INFO HaplotypeCaller - Shutting down engine

[December 7, 2021 at 3:34:28 PM CET] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 13.99 minutes.

Runtime.totalMemory()=6543114240

• How I got there: I first dowloaded the SRA file of the WGS sequencing of a single sample from NCBI. Then used SRA tool to convert it to bam file.

sam-dump "$TMPDIR"/SRR8788980.1 | samtools view -bS - > "$TMPDIR"/output_dir/SRR8788980.1.bam

Then downloaded the reference genome using the URL from the header in the bam file. I made sure the naming of chromosomes are consistent in bam files and reference genome (1,2,3,..). 

Then I used picard and samtools to generate index files for the reference genome. And because gatk told me the index of the bam file was not complete, I had to use

samtools index SRR8788980.1.bam 

command to generate index file of the sample. Then the program seemed to be working properly. But I had no idea why there was nothing in the output file. Could you help me figure out what is going wrong here? 

Appreciate!