Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.d92c8321 [Wed Oct 24 22:24:01 UTC 2018] picard.sam.MergeSamFiles INPUT=[gs:/fc-secure-112b7788-7c21-414f-84de-577174761638/181022/HC7WVDSXX_2_SL359216.unmapped.bam, gs:/fc-secure-112b7788-7c21-414f-84de-577174761638/181022/HCGMJDSXX_3_SL359216.unmapped.bam, gs:/fc-secure-112b7788-7c21-414f-84de-577174761638/181022/HC7WVDSXX_3_SL359216.unmapped.bam, gs:/fc-secure-112b7788-7c21-414f-84de-577174761638/181022/HCGMJDSXX_1_SL359216.unmapped.bam, gs:/fc-secure-112b7788-7c21-414f-84de-577174761638/181022/HCGMJDSXX_4_SL359216.unmapped.bam, gs:/fc-secure-112b7788-7c21-414f-84de-577174761638/181022/HCGMJDSXX_2_SL359216.unmapped.bam] OUTPUT=5644-DB-0002_201853055.unmapped.bam SORT_ORDER=queryname ASSUME_SORTED=true USE_THREADING=true MERGE_SEQUENCE_DICTIONARIES=false 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 [Wed Oct 24 22:24:01 UTC 2018] Executing as root@c3e29f92fdee on Linux 4.9.0-0.bpo.6-amd64 amd64; OpenJDK 64-Bit Server VM 1.8.0_111-8u111-b14-2~bpo8+1-b14; Picard version: 2.8.3-SNAPSHOT [Wed Oct 24 22:24:01 UTC 2018] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=204996608 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: /cromwell_root/gs:/fc-secure-112b7788-7c21-414f-84de-577174761638/181022/HC7WVDSXX_2_SL359216.unmapped.bam at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:338) at htsjdk.samtools.util.IOUtil.assertFileIsReadable(IOUtil.java:325) at picard.sam.MergeSamFiles.doWork(MergeSamFiles.java:141) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:205) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:94) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:104)