Can you please provide
a) GATK version used: GATK4

b) Exact GATK commands used:

Using v2.7.0 of the 1-Mutect2_PON walkthrough

c) The entire error log if applicable.

I'm running the GATK Best Practices workspace for 1-Mutect2_PON to generate a panel of normals from 37 of my samples, and it seems that each of my shards has an error finding the necessary file location for output like the following:

Required file output '/cromwell_root/normal-pileups.table' does not exist.

Required file output '/cromwell_root/output.vcf.stats' does not exist.

Required file output '/cromwell_root/tumor-pileups.table' does not exist.

The full log from one of the shards is below:

2020/03/07 21:11:23 Starting container setup. 2020/03/07 21:11:26 Done container setup. 2020/03/07 21:11:27 Starting localization. 2020/03/07 21:11:38 Localization script execution started... 2020/03/07 21:11:38 Localizing input gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/bec4f358-cc22-485c-a054-e19907c924fd/Mutect2_Panel/d93f8133-c8b7-4ad1-b05b-b7a23b21c409/call-Mutect2/shard-4/Mutect2/ae4c6a74-231e-449d-99b0-acbd2d6b13db/call-M2/shard-1/script -> /cromwell_root/script 2020/03/07 21:11:39 Localization script execution complete. 2020/03/07 21:11:44 Done localization. 2020/03/07 21:11:45 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint= us.gcr.io/broad-gatk/gatk@sha256:cec850f20311f0686fcf88510bc44e529590d78bec7076a603132115943c09e6 /bin/bash /cromwell_root/script Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.9f99cab3 21:11:58.620 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 21:11:59.749 INFO GetSampleName - ------------------------------------------------------------ 21:11:59.750 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.1.4.0 21:11:59.750 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/ 21:11:59.751 INFO GetSampleName - Executing as root@78ed1bcf7cbf on Linux v4.19.87+ amd64 21:11:59.752 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03 21:11:59.752 INFO GetSampleName - Start Date/Time: March 7, 2020 9:11:58 PM UTC 21:11:59.753 INFO GetSampleName - ------------------------------------------------------------ 21:11:59.753 INFO GetSampleName - ------------------------------------------------------------ 21:11:59.758 INFO GetSampleName - HTSJDK Version: 2.20.3 21:11:59.758 INFO GetSampleName - Picard Version: 2.21.1 21:11:59.759 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2 21:11:59.759 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 21:11:59.759 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 21:11:59.760 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 21:11:59.760 INFO GetSampleName - Deflater: IntelDeflater 21:11:59.760 INFO GetSampleName - Inflater: IntelInflater 21:11:59.761 INFO GetSampleName - GCS max retries/reopens: 20 21:11:59.761 INFO GetSampleName - Requester pays: disabled 21:11:59.761 WARN GetSampleName - [1m[31m !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: GetSampleName is a BETA tool and is not yet ready for use in production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!![0m 21:11:59.762 INFO GetSampleName - Initializing engine 21:12:06.683 INFO GetSampleName - Done initializing engine 21:12:06.704 INFO ProgressMeter - Starting traversal 21:12:06.704 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute 21:12:06.725 INFO ProgressMeter - unmapped 0.0 0 NaN 21:12:06.727 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes. 21:12:06.727 INFO GetSampleName - Shutting down engine [March 7, 2020 9:12:07 PM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.16 minutes. Runtime.totalMemory()=245301248 Using GATK jar /root/gatk.jar defined in environment variable GATK_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 -Xmx3000m -jar /root/gatk.jar GetSampleName -R gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -I gs://fc-32eb6e4f-33a6-4972-9042-520606ee423e/thalassemia_bams/M_CH_041.bam -O tumor_name.txt -encode Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.9f99cab3 21:12:13.251 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 21:12:13.647 INFO Mutect2 - ------------------------------------------------------------ 21:12:13.650 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.4.0 21:12:13.651 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/ 21:12:13.651 INFO Mutect2 - Executing as root@78ed1bcf7cbf on Linux v4.19.87+ amd64 21:12:13.652 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03 21:12:13.652 INFO Mutect2 - Start Date/Time: March 7, 2020 9:12:13 PM UTC 21:12:13.653 INFO Mutect2 - ------------------------------------------------------------ 21:12:13.653 INFO Mutect2 - ------------------------------------------------------------ 21:12:13.654 INFO Mutect2 - HTSJDK Version: 2.20.3 21:12:13.654 INFO Mutect2 - Picard Version: 2.21.1 21:12:13.654 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2 21:12:13.654 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 21:12:13.655 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 21:12:13.655 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 21:12:13.655 INFO Mutect2 - Deflater: IntelDeflater 21:12:13.656 INFO Mutect2 - Inflater: IntelInflater 21:12:13.656 INFO Mutect2 - GCS max retries/reopens: 20 21:12:13.657 INFO Mutect2 - Requester pays: disabled 21:12:13.657 INFO Mutect2 - Initializing engine 21:12:21.021 INFO FeatureManager - Using codec IntervalListCodec to read file gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/bec4f358-cc22-485c-a054-e19907c924fd/Mutect2_Panel/d93f8133-c8b7-4ad1-b05b-b7a23b21c409/call-Mutect2/shard-4/Mutect2/ae4c6a74-231e-449d-99b0-acbd2d6b13db/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0001-scattered.interval_list 21:12:22.291 INFO IntervalArgumentCollection - Processing 3937534 bp from intervals 21:12:22.459 INFO Mutect2 - Done initializing engine 21:12:23.110 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_utils.so 21:12:23.229 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so 21:12:23.338 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM 21:12:23.339 INFO IntelPairHmm - Available threads: 1 21:12:23.339 INFO IntelPairHmm - Requested threads: 4 21:12:23.340 WARN IntelPairHmm - Using 1 available threads, but 4 were requested 21:12:23.345 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation 21:12:23.631 INFO ProgressMeter - Starting traversal 21:12:23.631 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute 21:12:36.265 INFO ProgressMeter - chr1:247965590 0.2 10 47.5 21:12:48.432 INFO ProgressMeter - chr1:248573829 0.4 130 314.5 21:13:02.254 INFO ProgressMeter - chr2:1137622 0.6 280 435.0 21:13:13.202 INFO ProgressMeter - chr2:5694042 0.8 480 581.0 21:13:24.188 INFO ProgressMeter - chr2:9854326 1.0 710 703.5 21:13:35.036 INFO ProgressMeter - chr2:15424315 1.2 1040 873.9 21:13:46.374 INFO ProgressMeter - chr2:19935560 1.4 1230 891.9 21:13:56.507 INFO ProgressMeter - chr2:24175481 1.5 1540 995.0 21:14:06.581 INFO ProgressMeter - chr2:26316912 1.7 1900 1107.3 21:14:17.858 INFO ProgressMeter - chr2:28783907 1.9 2620 1376.2 21:14:28.785 INFO ProgressMeter - chr2:32128408 2.1 2930 1404.7 21:14:39.075 INFO ProgressMeter - chr2:37372356 2.3 3380 1497.3 21:14:51.330 INFO ProgressMeter - chr2:42048200 2.5 3640 1478.7 21:15:02.409 INFO ProgressMeter - chr2:45008845 2.6 4000 1511.6 21:15:13.938 INFO ProgressMeter - chr2:50236789 2.8 4330 1525.5 21:15:24.173 INFO ProgressMeter - chr2:54869181 3.0 4550 1512.1 21:15:34.869 INFO ProgressMeter - chr2:60461762 3.2 4840 1518.5 21:15:47.045 INFO ProgressMeter - chr2:64636827 3.4 5260 1551.5 21:15:57.098 INFO ProgressMeter - chr2:69470989 3.6 5550 1560.0 21:16:08.182 INFO ProgressMeter - chr2:71686454 3.7 5960 1592.5 21:16:18.263 INFO ProgressMeter - chr2:74523310 3.9 6470 1654.5 21:16:28.941 INFO ProgressMeter - chr2:79026713 4.1 6650 1626.5 21:16:38.946 INFO ProgressMeter - chr2:86049160 4.3 7040 1654.4 21:16:49.680 INFO ProgressMeter - chr2:91442804 4.4 7420 1673.4 21:16:59.681 INFO ProgressMeter - chr2:96699932 4.6 7860 1708.4 21:17:10.679 INFO ProgressMeter - chr2:98194361 4.8 8210 1716.1 21:17:20.752 INFO ProgressMeter - chr2:101421240 5.0 8650 1746.8 21:17:30.796 INFO ProgressMeter - chr2:106138728 5.1 8920 1742.4 21:17:41.301 INFO ProgressMeter - chr2:110805263 5.3 9370 1769.8 21:17:52.010 INFO ProgressMeter - chr2:113951479 5.5 9840 1797.9 21:18:02.812 INFO ProgressMeter - chr2:118974333 5.7 9960 1761.9 21:18:03.437 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.064111557 21:18:03.438 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 11.019498010000001 21:18:03.438 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 9.99 sec 21:18:03.439 INFO Mutect2 - Shutting down engine [March 7, 2020 9:18:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 5.84 minutes. Runtime.totalMemory()=466550784 java.lang.IllegalArgumentException: Cannot construct fragment from more than two reads at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:725) at org.broadinstitute.hellbender.utils.read.Fragment.create(Fragment.java:36) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) at org.broadinstitute.hellbender.utils.genotyper.AlleleLikelihoods.groupEvidence(AlleleLikelihoods.java:595) at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.callMutations(SomaticGenotypingEngine.java:93) at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.callRegion(Mutect2Engine.java:251) at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.apply(Mutect2.java:320) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:308) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:281) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206) at org.broadinstitute.hellbender.Main.main(Main.java:292) Using GATK jar /root/gatk.jar defined in environment variable GATK_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 -Xmx3000m -jar /root/gatk.jar Mutect2 -R gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -I gs://fc-32eb6e4f-33a6-4972-9042-520606ee423e/thalassemia_bams/M_CH_041.bam -tumor M_CH_041 -L gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/bec4f358-cc22-485c-a054-e19907c924fd/Mutect2_Panel/d93f8133-c8b7-4ad1-b05b-b7a23b21c409/call-Mutect2/shard-4/Mutect2/ae4c6a74-231e-449d-99b0-acbd2d6b13db/call-SplitIntervals/cacheCopy/glob-0fc990c5ca95eebc97c4c204e3e303e1/0001-scattered.interval_list -O output.vcf --max-mnp-distance 0 2020/03/07 21:18:04 Starting delocalization. 2020/03/07 21:18:05 Delocalization script execution started... 2020/03/07 21:18:05 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/bec4f358-cc22-485c-a054-e19907c924fd/Mutect2_Panel/d93f8133-c8b7-4ad1-b05b-b7a23b21c409/call-Mutect2/shard-4/Mutect2/ae4c6a74-231e-449d-99b0-acbd2d6b13db/call-M2/shard-1/memory_retry_rc 2020/03/07 21:18:05 Delocalizing output /cromwell_root/rc -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/bec4f358-cc22-485c-a054-e19907c924fd/Mutect2_Panel/d93f8133-c8b7-4ad1-b05b-b7a23b21c409/call-Mutect2/shard-4/Mutect2/ae4c6a74-231e-449d-99b0-acbd2d6b13db/call-M2/shard-1/rc 2020/03/07 21:18:07 Delocalizing output /cromwell_root/stdout -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/bec4f358-cc22-485c-a054-e19907c924fd/Mutect2_Panel/d93f8133-c8b7-4ad1-b05b-b7a23b21c409/call-Mutect2/shard-4/Mutect2/ae4c6a74-231e-449d-99b0-acbd2d6b13db/call-M2/shard-1/stdout 2020/03/07 21:18:08 Delocalizing output /cromwell_root/stderr -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/bec4f358-cc22-485c-a054-e19907c924fd/Mutect2_Panel/d93f8133-c8b7-4ad1-b05b-b7a23b21c409/call-Mutect2/shard-4/Mutect2/ae4c6a74-231e-449d-99b0-acbd2d6b13db/call-M2/shard-1/stderr 2020/03/07 21:18:11 Delocalizing output /cromwell_root/normal-pileups.table -> gs://fc-1bf984ac-6958-4b2c-9982-a3ba625d86c6/bec4f358-cc22-485c-a054-e19907c924fd/Mutect2_Panel/d93f8133-c8b7-4ad1-b05b-b7a23b21c409/call-Mutect2/shard-4/Mutect2/ae4c6a74-231e-449d-99b0-acbd2d6b13db/call-M2/shard-1/normal-pileups.table Required file output '/cromwell_root/normal-pileups.table' does not exist.