Hello,
My FireCloud analysis using method PreProcessingForVariantDiscovery_GATK4 (copied from Method repository: Snapshot 8), keeps failing during the SoftAndFixTags.log step. Failure seems to be due to copying outputs to Google Buckets. All other steps prior to SoftAndFixTags work without error (see attached screenshot). Would greatly appreciate any help on why I am experiencing this failure.
I have shared the workspace I am running in 'MC-preprocessGATK4' with GROUP_FireCloud-Support@firecloud.org, and am copying content from SoftAndFixTags.log below. Happy to provide any additional info required.
Thank you in advance,
2019/05/24 16:12:03 Starting container setup.
2019/05/24 16:12:10 Done container setup.
2019/05/24 16:12:15 Starting localization.
2019/05/24 16:12:21 Localizing input gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-MarkDuplicates/hd753rep1.hg38.aligned.unsorted.duplicates_marked.bam -> /cromwell_root/fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-MarkDuplicates/hd753rep1.hg38.aligned.unsorted.duplicates_marked.bam
2019/05/24 16:13:01 Localizing input gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta -> /cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta
2019/05/24 16:14:03 Localizing input gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dict -> /cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.dict
2019/05/24 16:14:16 Localizing input gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai -> /cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai
2019/05/24 16:14:23 Localizing input gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/script -> /cromwell_root/script
2019/05/24 16:14:30 Done localization.
2019/05/24 16:14:36 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint= broadinstitute/genomes-in-the-cloud@sha256:039564efc566e62526627b023847d92fd0c98676988f99cbb1f4135509ecb1f8 /bin/bash /cromwell_root/script
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.5f968c15
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.5f968c15
ERROR StatusLogger No log4j2 configuration file found. Using default configuration: logging only errors to the console.ERROR StatusLogger No log4j2 configuration file found. Using default configuration: logging only errors to the console.
[Fri May 24 16:14:45 UTC 2019] picard.sam.SortSam INPUT=/cromwell_root/fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-MarkDuplicates/hd753rep1.hg38.aligned.unsorted.duplicates_marked.bam OUTPUT=/dev/stdout SORT_ORDER=coordinate CREATE_INDEX=false CREATE_MD5_FILE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Fri May 24 16:14:45 UTC 2019] Executing as root@d3b07c2379a8 on Linux 4.14.119+ amd64; OpenJDK 64-Bit Server VM 1.8.0_111-8u111-b14-2~bpo8+1-b14; Deflater: Intel; Inflater: Intel; Picard version: 2.10.5-SNAPSHOT
[Fri May 24 16:14:45 UTC 2019] picard.sam.SetNmAndUqTags INPUT=/dev/stdin OUTPUT=hd753rep1.hg38.aligned.duplicate_marked.sorted.bam CREATE_INDEX=true CREATE_MD5_FILE=true REFERENCE_SEQUENCE=/cromwell_root/broad-references/hg38/v0/Homo_sapiens_assembly38.fasta IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Fri May 24 16:14:45 UTC 2019] Executing as root@d3b07c2379a8 on Linux 4.14.119+ amd64; OpenJDK 64-Bit Server VM 1.8.0_111-8u111-b14-2~bpo8+1-b14; Deflater: Intel; Inflater: Intel; Picard version: 2.10.5-SNAPSHOT
INFO 2019-05-24 16:16:29 SortSam Read 10,000,000 records. Elapsed time: 00:01:42s. Time for last 10,000,000: 102s. Last read position: chr4:54,280,302
INFO 2019-05-24 16:18:10 SortSam Read 20,000,000 records. Elapsed time: 00:03:23s. Time for last 10,000,000: 100s. Last read position: chr8:92,017,216
INFO 2019-05-24 16:19:31 SortSam Finished reading inputs, merging and writing to output now.
INFO 2019-05-24 16:23:56 SortSam Wrote 10,000,000 records from a sorting collection. Elapsed time: 00:09:09s. Time for last 10,000,000: 262s. Last read position: chr6:106,107,103
[Fri May 24 16:39:26 UTC 2019] picard.sam.SetNmAndUqTags done. Elapsed time: 24.72 minutes.
Runtime.totalMemory()=506986496
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:517)
at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:455)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:445)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:194)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:326)
at java.io.DataInputStream.read(DataInputStream.java:149)
at htsjdk.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:404)
at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:380)
at htsjdk.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:366)
at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:209)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:829)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:803)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at picard.sam.SetNmMdAndUqTags.doWork(SetNmMdAndUqTags.java:107)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:228)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)
2019/05/24 16:39:36 Starting delocalization.
2019/05/24 16:39:41 Delocalizing output /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam -> gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam
2019/05/24 16:39:59 Delocalizing output /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bai -> gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/hd753rep1.hg38.aligned.duplicate_marked.sorted.bai
2019/05/24 16:40:06 Delocalizing output /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam.md5 -> gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam.md5
2019/05/24 16:40:08 rm -f $HOME/.config/gcloud/gce && gsutil cp /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam.md5 gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/ failed
CommandException: No URLs matched: /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam.md5
2019/05/24 16:40:08 Waiting 5 seconds and retrying
2019/05/24 16:40:14 rm -f $HOME/.config/gcloud/gce && gsutil cp /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam.md5 gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/ failed
CommandException: No URLs matched: /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam.md5
2019/05/24 16:40:14 Waiting 5 seconds and retrying
2019/05/24 16:40:20 rm -f $HOME/.config/gcloud/gce && gsutil cp /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam.md5 gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/ failed
CommandException: No URLs matched: /cromwell_root/hd753rep1.hg38.aligned.duplicate_marked.sorted.bam.md5
2019/05/24 16:40:25 Delocalizing output /cromwell_root/stdout -> gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/stdout
2019/05/24 16:40:32 Delocalizing output /cromwell_root/stderr -> gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/stderr
2019/05/24 16:40:40 Delocalizing output /cromwell_root/rc -> gs://fc-c9d6903a-b0e5-4e53-a36c-99cfd31f9a53/c9ef0454-8b5a-4647-b527-89c260be19e3/PreProcessingForVariantDiscovery_GATK4/4eae049a-317b-41a6-8845-9a5b9c645ce0/call-SortAndFixTags/rc