Error "Could not create tar.gz file" for Mutect2 --f1r2-tar-gz
Hi, I am trying to run Mutect2 and getting an error "Could not create tar.gz file" based on the --f1r2-tar-gz flag.
GATK version is gatk-4.2.5.0.
The exact command that I used is below:
gatk Mutect2 \I know for sure that the server I'm running this on has TAR:
-R $ref \
-L $interval \
-I $din/${sampleid}_bqsr.bam \
-germline-resource $germres \
-pon $pon \
--f1r2-tar-gz $dout/interim/${sampleid}_f1r2.tar.gz \
-O $dout/${sampleid}_bqsr.vcf
$ tar --version
tar (GNU tar) 1.26
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
Below is the entire log:
17:07:05.521 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/projects/b1131/saya/bbcar/tools/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Apr 27, 2022 5:07:05 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
17:07:05.965 INFO Mutect2 - ------------------------------------------------------------
17:07:05.966 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.2.5.0
17:07:05.966 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
17:07:05.968 INFO Mutect2 - Executing as srd6051@qnode0138 on Linux v3.10.0-862.el7.x86_64 amd64
17:07:05.968 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_302-b08
17:07:05.969 INFO Mutect2 - Start Date/Time: April 27, 2022 5:07:05 PM CDT
17:07:05.970 INFO Mutect2 - ------------------------------------------------------------
17:07:05.970 INFO Mutect2 - ------------------------------------------------------------
17:07:05.971 INFO Mutect2 - HTSJDK Version: 2.24.1
17:07:05.971 INFO Mutect2 - Picard Version: 2.25.4
17:07:05.971 INFO Mutect2 - Built for Spark Version: 2.4.5
17:07:05.971 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:07:05.971 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:07:05.971 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:07:05.971 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:07:05.971 INFO Mutect2 - Deflater: IntelDeflater
17:07:05.972 INFO Mutect2 - Inflater: IntelInflater
17:07:05.972 INFO Mutect2 - GCS max retries/reopens: 20
17:07:05.972 INFO Mutect2 - Requester pays: disabled
17:07:05.972 INFO Mutect2 - Initializing engine
17:07:06.975 INFO FeatureManager - Using codec VCFCodec to read file file:///projects/b1131/saya/bbcar/genome_resources/GATK/1000g_pon.hg38.vcf.gz
17:07:07.595 INFO FeatureManager - Using codec VCFCodec to read file file:///projects/b1131/saya/bbcar/genome_resources/GATK/af-only-gnomad.hg38.vcf.gz
17:07:07.873 INFO FeatureManager - Using codec IntervalListCodec to read file file:///projects/b1122/gannon/bbcar/RAW_data/int_lst/SureSelect_v6/hg38.preprocessed.interval_list
17:07:10.971 INFO IntervalArgumentCollection - Processing 133370321 bp from intervals
17:07:11.448 INFO Mutect2 - Done initializing engine
17:07:11.542 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/projects/b1131/saya/bbcar/tools/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
17:07:11.555 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/projects/b1131/saya/bbcar/tools/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
17:07:11.624 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
17:07:11.627 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
17:07:11.628 INFO IntelPairHmm - Available threads: 1
17:07:11.628 INFO IntelPairHmm - Requested threads: 4
17:07:11.628 WARN IntelPairHmm - Using 1 available threads, but 4 were requested
17:07:11.629 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
17:07:12.012 INFO ProgressMeter - Starting traversal
17:07:12.013 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
17:07:22.157 INFO ProgressMeter - chr1:1640327 0.2 870 5146.4
17:07:32.177 INFO ProgressMeter - chr1:15495621 0.3 5280 15711.2
17:07:42.177 INFO ProgressMeter - chr1:31727168 0.5 11300 22477.1
17:07:52.180 INFO ProgressMeter - chr1:84479030 0.7 22140 33071.9
17:08:02.192 INFO ProgressMeter - chr1:155199552 0.8 33530 40093.3
17:08:12.193 INFO ProgressMeter - chr1:196227972 1.0 42540 42412.8
17:08:22.213 INFO ProgressMeter - chr10:7220159 1.2 55150 47136.8
17:08:32.355 INFO ProgressMeter - chr11:207427 1.3 76810 57362.3
17:08:42.373 INFO ProgressMeter - chr11:17547423 1.5 82560 54821.3
17:08:52.403 INFO ProgressMeter - chr11:65620926 1.7 92160 55081.2
17:09:02.438 INFO ProgressMeter - chr11:126276739 1.8 105560 57356.6
17:09:12.457 INFO ProgressMeter - chr12:56128668 2.0 120420 59988.5
17:09:22.528 INFO ProgressMeter - chr12:130839126 2.2 135920 62484.8
17:09:32.538 INFO ProgressMeter - chr14:69332833 2.3 156410 66782.4
17:09:42.546 INFO ProgressMeter - chr15:43042963 2.5 170340 67894.7
17:09:52.546 INFO ProgressMeter - chr16:871079 2.7 185600 69368.9
17:10:02.592 INFO ProgressMeter - chr16:29102148 2.8 194630 68459.8
17:10:12.595 INFO ProgressMeter - chr16:71649723 3.0 203120 67488.5
17:10:22.610 INFO ProgressMeter - chr17:7759443 3.2 211490 66577.1
17:10:32.688 INFO ProgressMeter - chr17:42963854 3.3 223150 66719.8
17:10:42.688 INFO ProgressMeter - chr18:2667220 3.5 237300 67582.8
17:10:52.720 INFO ProgressMeter - chr18:10548803 3.7 238690 64888.7
17:11:02.794 INFO ProgressMeter - chr19:814182 3.8 247030 64224.5
17:11:12.822 INFO ProgressMeter - chr19:1816949 4.0 248160 61831.6
17:11:22.825 INFO ProgressMeter - chr19:3638632 4.2 249510 59688.5
17:11:32.851 INFO ProgressMeter - chr19:5033018 4.3 250700 57668.0
17:11:42.919 INFO ProgressMeter - chr19:7606319 4.5 252470 55916.8
17:11:52.929 INFO ProgressMeter - chr19:17533403 4.7 258840 55284.9
17:12:02.940 INFO ProgressMeter - chr19:42407545 4.8 267100 55086.0
17:12:12.951 INFO ProgressMeter - chr19:54095269 5.0 274180 54665.1
17:12:22.968 INFO ProgressMeter - chr2:70692648 5.2 288390 55646.5
17:12:32.969 INFO ProgressMeter - chr2:218751452 5.3 312730 58462.4
17:12:42.977 INFO ProgressMeter - chr20:46350742 5.5 327690 59406.6
17:12:52.984 INFO ProgressMeter - chr22:41172247 5.7 345970 60879.7
17:13:02.994 INFO ProgressMeter - chr3:48691151 5.8 358290 61249.5
17:13:13.005 INFO ProgressMeter - chr3:128081492 6.0 370200 61530.4
17:13:23.031 INFO ProgressMeter - chr4:8218295 6.2 383920 62086.5
17:13:33.092 INFO ProgressMeter - chr5:423077 6.4 403900 63593.3
17:13:43.111 INFO ProgressMeter - chr5:14755909 6.5 406050 62293.8
17:13:53.136 INFO ProgressMeter - chr5:38921663 6.7 408490 61102.0
17:14:03.138 INFO ProgressMeter - chr5:149867473 6.9 423670 61830.8
17:14:13.170 INFO ProgressMeter - chr6:13227565 7.0 431300 61445.0
17:14:23.200 INFO ProgressMeter - chr6:33665218 7.2 436750 60774.2
17:14:33.219 INFO ProgressMeter - chr6:144835626 7.4 452840 61582.3
17:14:43.221 INFO ProgressMeter - chr7:76265413 7.5 467890 62218.3
17:14:53.221 INFO ProgressMeter - chr8:27293828 7.7 487870 63468.5
17:15:03.279 INFO ProgressMeter - chr9:5769073 7.9 503810 64143.4
17:15:13.322 INFO ProgressMeter - chr9:26946645 8.0 506020 63080.6
17:15:23.345 INFO ProgressMeter - chr9:35616291 8.2 507760 62006.1
17:15:33.364 INFO ProgressMeter - chr9:130904001 8.4 521610 62424.9
17:15:43.370 INFO ProgressMeter - chrX:70610551 8.5 534380 62701.4
17:15:47.972 INFO Mutect2 - 431002 read(s) filtered by: MappingQualityReadFilter
0 read(s) filtered by: MappingQualityAvailableReadFilter
0 read(s) filtered by: MappingQualityNotZeroReadFilter
0 read(s) filtered by: MappedReadFilter
11296 read(s) filtered by: NotSecondaryAlignmentReadFilter
2641322 read(s) filtered by: NotDuplicateReadFilter
0 read(s) filtered by: PassesVendorQualityCheckReadFilter
0 read(s) filtered by: NonChimericOriginalAlignmentReadFilter
0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
0 read(s) filtered by: ReadLengthReadFilter
0 read(s) filtered by: GoodCigarReadFilter
0 read(s) filtered by: WellformedReadFilter
3083620 total reads filtered
17:15:47.974 INFO ProgressMeter - chrY:25987861 8.6 545361 63418.9
17:15:47.974 INFO ProgressMeter - Traversal complete. Processed 545361 total regions in 8.6 minutes.
17:15:48.697 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.225482335
17:15:48.697 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 11.492043034
17:15:48.697 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 36.77 sec
17:15:48.701 INFO Mutect2 - Shutting down engine
[April 27, 2022 5:15:48 PM CDT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 8.72 minutes.
Runtime.totalMemory()=385929216
***********************************************************************
A USER ERROR has occurred: Could not create tar.gz file
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /projects/b1131/saya/bbcar/tools/gatk-4.2.5.0/gatk-package-4.2.5.0-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 -jar /projects/b1131/saya/bbcar/tools/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar Mutect2 -R /projects/p30791/hg38_ref/hg38.fa -L /projects/b1122/gannon/bbcar/RAW_data/int_lst/SureSelect_v6/hg38.preprocessed.interval_list -I /projects/b1131/saya/bbcar/01_alignment/tissue/aligned/1004t_bqsr.bam -germline-resource /projects/b1131/saya/bbcar/genome_resources/GATK/af-only-gnomad.hg38.vcf.gz -pon /projects/b1131/saya/bbcar/genome_resources/GATK/1000g_pon.hg38.vcf.gz --f1r2-tar-gz /projects/b1131/saya/bbcar/02_variant_calls/interim/1004t_f1r2.tar.gz -O /projects/b1131/saya/bbcar/02_variant_calls/1004t_bqsr.vcf
When I remove the --f1r2-tar-gz flag, the program runs successfully without any errors. Any input would be appreciated!
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First thought that comes to mind: You are specifying a folder structure to place the f1r2 output.
--f1r2-tar-gz $dout/interim/${sampleid}_f1r2.tar.gzDid you make sure that the folder interim exists? The mutect2 call should maybe be preceded by
mkdir $dout/interim
Best,
Philipp
-
Philipp,
Wow, thank you so much! That did it. This was probably something I should have figured out on my own. I really appreciate your prompt response.
Best,
Saya
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Thanks for helping to find a solution Philipp Hähnel! And thanks for posting Saya Rene Dennis, I'm sure this will help out other users in the future.
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3 comments