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Process NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS (joint_variant_calling) terminated with an error exit status (3) #938

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nagihayate opened this issue Feb 11, 2023 · 16 comments
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Process NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS (joint_variant_calling) terminated with an error exit status (3) #938

nagihayate opened this issue Feb 11, 2023 · 16 comments
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@nagihayate
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Description of the bug

When i adding paramaters(--tools mutect2,haplotypecaller --joint_germline) to the process, there is an error in "MERGE_GENOTYPEGVCFS (joint_variant_calling)". And i can't found the right place to fix this problem.

Command used and terminal output

Pipeline completed with errors-
Error executing process > 'NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS (joint_variant_calling)'

Caused by:
  Process `NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS (joint_variant_calling)` terminated with an error exit status (3)

Command executed:

  gatk --java-options "-Xmx36g" MergeVcfs \
      --INPUT [chr4_31832570-32833016.vcf.gz].sort.vcf.gz --INPUT [chr21_9246088-9377143.vcf.gz].sort.vcf.gz --INPUT [chr9_63968448-64135013.vcf.gz].sort.vcf.gz --INPUT [chr18_10001-15410899.vcf.gz].sort.vcf.gz --INPUT [chr21_5443559-5449012.vcf.gz].sort.vcf.gz --INPUT [chr6_95070791-167591393.vcf.gz].sort.vcf.gz --INPUT [chr22_10834644-10874572.vcf.gz].sort.vcf.gz --INPUT [chr22_18339130-18433513.vcf.gz].sort.vcf.gz --INPUT [chr21_12965809-43212462.vcf.gz].sort.vcf.gz --INPUT [chr10_39230137-39409792.vcf.gz].sort.vcf.gz --INPUT [chr4_49486925-49658100.vcf.gz].sort.vcf.gz --INPUT [chr22_12275589-12438690.vcf.gz].sort.vcf.gz --INPUT [chr16_46380683-90228345.vcf.gz].sort.vcf.gz --INPUT [chr22_11118988-11160921.vcf.gz].sort.vcf.gz --INPUT [chr1_228608365-248946422.vcf.gz].sort.vcf.gz --INPUT [chrY_10682443-10691573.vcf.gz].sort.vcf.gz --INPUT [chr4_8816478-9272916.vcf.gz].sort.vcf.gz --INPUT [chr3_90568829-90722458.vcf.gz].sort.vcf.gz --INPUT [chr21_43262463-46699983.vcf.gz].sort.vcf.gz --INPUT [chr18_54537529-80263285.vcf.gz].sort.vcf.gz --INPUT [chr11_71055697-87978202.vcf.gz].sort.vcf.gz --INPUT [chr10_124121503-133690466.vcf.gz].sort.vcf.gz --INPUT [chr17_491112-21795850.vcf.gz].sort.vcf.gz --INPUT [chr13_111843442-113673020.vcf.gz].sort.vcf.gz --INPUT [chr12_10001-7083650.vcf.gz].sort.vcf.gz --INPUT [chr12_7084651-34719407.vcf.gz].sort.vcf.gz --INPUT [chr4_10001-1429358.vcf.gz].sort.vcf.gz --INPUT [chr21_8099840-8260971.vcf.gz].sort.vcf.gz --INPUT [chr9_134185537-138334717.vcf.gz].sort.vcf.gz --INPUT [chr9_63008372-63202862.vcf.gz].sort.vcf.gz --INPUT [chr8_7667128-12234345.vcf.gz].sort.vcf.gz --INPUT [chrY_56673215-56771509.vcf.gz].sort.vcf.gz --INPUT [chr21_10324328-10814560.vcf.gz].sort.vcf.gz --INPUT [chr2_91402512-92138145.vcf.gz].sort.vcf.gz --INPUT [chr11_51078349-54425074.vcf.gz].sort.vcf.gz --INPUT [chr10_38573339-38906036.vcf.gz].sort.vcf.gz --INPUT [chr1_125173584-125184587.vcf.gz].sort.vcf.gz --INPUT [chr8_85714223-145078636.vcf.gz].sort.vcf.gz --INPUT [chr6_167641394-170745979.vcf.gz].sort.vcf.gz --INPUT [chr9_10001-41225986.vcf.gz].sort.vcf.gz --INPUT [chr9_61785369-62149738.vcf.gz].sort.vcf.gz --INPUT [chr20_29413578-29562970.vcf.gz].sort.vcf.gz --INPUT [chr2_97489619-238903659.vcf.gz].sort.vcf.gz --INPUT [chr14_16133336-16140527.vcf.gz].sort.vcf.gz --INPUT [chr16_18486487-33214595.vcf.gz].sort.vcf.gz --INPUT [chr20_29697631-30038348.vcf.gz].sort.vcf.gz --INPUT [chrY_9055175-9057608.vcf.gz].sort.vcf.gz --INPUT [chr5_46485901-47069162.vcf.gz].sort.vcf.gz --INPUT [chr20_60001-63215.vcf.gz].sort.vcf.gz --INPUT [chr4_49708101-51743951.vcf.gz].sort.vcf.gz --INPUT [chr22_49975366-50808468.vcf.gz].sort.vcf.gz --INPUT [chr9_43236168-43263290.vcf.gz].sort.vcf.gz --INPUT [chr5_49666174-50059807.vcf.gz].sort.vcf.gz --INPUT [chrY_11013047-11016992.vcf.gz].sort.vcf.gz --INPUT [chr20_31161626-36314371.vcf.gz].sort.vcf.gz --INPUT [chr8_12284346-43983744.vcf.gz].sort.vcf.gz --INPUT [chr22_12691731-12726204.vcf.gz].sort.vcf.gz --INPUT [chr12_132224363-133265309.vcf.gz].sort.vcf.gz --INPUT [chr16_34339330-34521510.vcf.gz].sort.vcf.gz --INPUT [chr18_47019913-54536574.vcf.gz].sort.vcf.gz --INPUT [chr2_92188146-94090557.vcf.gz].sort.vcf.gz --INPUT [chr1_10001-207666.vcf.gz].sort.vcf.gz --INPUT [chr16_34580966-34584085.vcf.gz].sort.vcf.gz --INPUT [chr2_32917626-89330679.vcf.gz].sort.vcf.gz --INPUT [chr21_5010001-5166246.vcf.gz].sort.vcf.gz --INPUT [chr16_10001-18436486.vcf.gz].sort.vcf.gz --INPUT [chr11_60001-50821348.vcf.gz].sort.vcf.gz --INPUT [chrX_144475607-156030895.vcf.gz].sort.vcf.gz --INPUT [chr4_58921382-190123121.vcf.gz].sort.vcf.gz --INPUT [chr19_24891357-24898313.vcf.gz].sort.vcf.gz --INPUT [chr20_28868453-28890335.vcf.gz].sort.vcf.gz --INPUT [chr9_66591388-67920552.vcf.gz].sort.vcf.gz --INPUT [chr13_18171249-18358106.vcf.gz].sort.vcf.gz --INPUT [chr7_58169654-60828234.vcf.gz].sort.vcf.gz --INPUT [chr2_89753993-90402511.vcf.gz].sort.vcf.gz --INPUT [chr5_49609715-49611721.vcf.gz].sort.vcf.gz --INPUT [chr13_18408107-86202979.vcf.gz].sort.vcf.gz --INPUT [chr17_21814104-21984549.vcf.gz].sort.vcf.gz --INPUT [chr17_26935981-81742542.vcf.gz].sort.vcf.gz --INPUT [chr20_30456078-30761898.vcf.gz].sort.vcf.gz --INPUT [chr22_11428057-11497337.vcf.gz].sort.vcf.gz --INPUT [chr8_45927266-85664222.vcf.gz].sort.vcf.gz --INPUT [chr21_8310972-8472360.vcf.gz].sort.vcf.gz --INPUT [chr5_155761325-181478259.vcf.gz].sort.vcf.gz --INPUT [chr21_7377866-7500890.vcf.gz].sort.vcf.gz --INPUT [chr20_31051509-31107036.vcf.gz].sort.vcf.gz --INPUT [chr2_10001-16145119.vcf.gz].sort.vcf.gz --INPUT [chr2_16146120-32867130.vcf.gz].sort.vcf.gz --INPUT [chr22_16302844-16304296.vcf.gz].sort.vcf.gz --INPUT [chr1_29553836-121976459.vcf.gz].sort.vcf.gz --INPUT [chr5_50109808-139452659.vcf.gz].sort.vcf.gz --INPUT [chr16_34584623-36260386.vcf.gz].sort.vcf.gz --INPUT [chrY_11674124-20207793.vcf.gz].sort.vcf.gz --INPUT [chr12_34829238-37185252.vcf.gz].sort.vcf.gz --INPUT [chr4_190173122-190204555.vcf.gz].sort.vcf.gz --INPUT [chr1_13004385-16799163.vcf.gz].sort.vcf.gz --INPUT [chr5_17580549-46435900.vcf.gz].sort.vcf.gz --INPUT [chrX_114331199-115738949.vcf.gz].sort.vcf.gz --INPUT [chr1_16849164-29552233.vcf.gz].sort.vcf.gz --INPUT [chrY_56821510-56887902.vcf.gz].sort.vcf.gz --INPUT [chr20_28752591-28843401.vcf.gz].sort.vcf.gz --INPUT [chr7_143700805-159335973.vcf.gz].sort.vcf.gz --INPUT [chr20_30088349-30425128.vcf.gz].sort.vcf.gz --INPUT [chr17_22813680-26627010.vcf.gz].sort.vcf.gz --INPUT [chr15_20729747-21193490.vcf.gz].sort.vcf.gz --INPUT [chr15_17000001-19725254.vcf.gz].sort.vcf.gz --INPUT [chr6_60001-58453888.vcf.gz].sort.vcf.gz --INPUT [chr10_47870369-124121200.vcf.gz].sort.vcf.gz --INPUT [chr22_11681289-11724629.vcf.gz].sort.vcf.gz --INPUT [chr9_41229379-41237752.vcf.gz].sort.vcf.gz --INPUT [chr20_29271827-29315342.vcf.gz].sort.vcf.gz --INPUT [chr11_88002897-135076622.vcf.gz].sort.vcf.gz --INPUT [chr7_61967064-61976104.vcf.gz].sort.vcf.gz --INPUT [chr16_33264596-33392411.vcf.gz].sort.vcf.gz --INPUT [chr3_10001-90565295.vcf.gz].sort.vcf.gz --INPUT [chr18_15791048-20564714.vcf.gz].sort.vcf.gz --INPUT [chrX_37285838-49348394.vcf.gz].sort.vcf.gz --INPUT [chr3_91256422-91257890.vcf.gz].sort.vcf.gz --INPUT [chr5_139453660-155760324.vcf.gz].sort.vcf.gz --INPUT [chr17_26698999-26720420.vcf.gz].sort.vcf.gz --INPUT [chr19_60001-24448980.vcf.gz].sort.vcf.gz --INPUT [chr22_12488691-12641730.vcf.gz].sort.vcf.gz --INPUT [chr13_86252980-111703855.vcf.gz].sort.vcf.gz --INPUT [chr1_143184588-223558935.vcf.gz].sort.vcf.gz --INPUT [chr21_10269869-10274327.vcf.gz].sort.vcf.gz --INPUT [chr1_122026460-124977944.vcf.gz].sort.vcf.gz --INPUT [chr6_61371373-95020790.vcf.gz].sort.vcf.gz --INPUT [chr15_84320067-101981189.vcf.gz].sort.vcf.gz --INPUT [chr8_60001-7617127.vcf.gz].sort.vcf.gz --INPUT [chrX_58605580-62412542.vcf.gz].sort.vcf.gz --INPUT [chr10_42066266-47780368.vcf.gz].sort.vcf.gz --INPUT [chr20_26436233-26590875.vcf.gz].sort.vcf.gz --INPUT [chr5_10001-17530548.vcf.gz].sort.vcf.gz \
      --OUTPUT joint_germline.vcf.gz \
      --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict \
      --TMP_DIR . \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS":
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
  END_VERSIONS

Command exit status:
  3

Command output:
  (empty)

Command error:
  Using GATK jar /opt/conda/envs/python27/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-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 -Xmx36g -jar /opt/conda/envs/python27/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar MergeVcfs --INPUT [chr4_31832570-32833016.vcf.gz].sort.vcf.gz --INPUT [chr21_9246088-9377143.vcf.gz].sort.vcf.gz --INPUT [chr9_63968448-64135013.vcf.gz].sort.vcf.gz --INPUT [chr18_10001-15410899.vcf.gz].sort.vcf.gz --INPUT [chr21_5443559-5449012.vcf.gz].sort.vcf.gz --INPUT [chr6_95070791-167591393.vcf.gz].sort.vcf.gz --INPUT [chr22_10834644-10874572.vcf.gz].sort.vcf.gz --INPUT [chr22_18339130-18433513.vcf.gz].sort.vcf.gz --INPUT [chr21_12965809-43212462.vcf.gz].sort.vcf.gz --INPUT [chr10_39230137-39409792.vcf.gz].sort.vcf.gz --INPUT [chr4_49486925-49658100.vcf.gz].sort.vcf.gz --INPUT [chr22_12275589-12438690.vcf.gz].sort.vcf.gz --INPUT [chr16_46380683-90228345.vcf.gz].sort.vcf.gz --INPUT [chr22_11118988-11160921.vcf.gz].sort.vcf.gz --INPUT [chr1_228608365-248946422.vcf.gz].sort.vcf.gz --INPUT [chrY_10682443-10691573.vcf.gz].sort.vcf.gz --INPUT [chr4_8816478-9272916.vcf.gz].sort.vcf.gz --INPUT [chr3_90568829-90722458.vcf.gz].sort.vcf.gz --INPUT [chr21_43262463-46699983.vcf.gz].sort.vcf.gz --INPUT [chr18_54537529-80263285.vcf.gz].sort.vcf.gz --INPUT [chr11_71055697-87978202.vcf.gz].sort.vcf.gz --INPUT [chr10_124121503-133690466.vcf.gz].sort.vcf.gz --INPUT [chr17_491112-21795850.vcf.gz].sort.vcf.gz --INPUT [chr13_111843442-113673020.vcf.gz].sort.vcf.gz --INPUT [chr12_10001-7083650.vcf.gz].sort.vcf.gz --INPUT [chr12_7084651-34719407.vcf.gz].sort.vcf.gz --INPUT [chr4_10001-1429358.vcf.gz].sort.vcf.gz --INPUT [chr21_8099840-8260971.vcf.gz].sort.vcf.gz --INPUT [chr9_134185537-138334717.vcf.gz].sort.vcf.gz --INPUT [chr9_63008372-63202862.vcf.gz].sort.vcf.gz --INPUT [chr8_7667128-12234345.vcf.gz].sort.vcf.gz --INPUT [chrY_56673215-56771509.vcf.gz].sort.vcf.gz --INPUT [chr21_10324328-10814560.vcf.gz].sort.vcf.gz --INPUT [chr2_91402512-92138145.vcf.gz].sort.vcf.gz --INPUT [chr11_51078349-54425074.vcf.gz].sort.vcf.gz --INPUT [chr10_38573339-38906036.vcf.gz].sort.vcf.gz --INPUT [chr1_125173584-125184587.vcf.gz].sort.vcf.gz --INPUT [chr8_85714223-145078636.vcf.gz].sort.vcf.gz --INPUT [chr6_167641394-170745979.vcf.gz].sort.vcf.gz --INPUT [chr9_10001-41225986.vcf.gz].sort.vcf.gz --INPUT [chr9_61785369-62149738.vcf.gz].sort.vcf.gz --INPUT [chr20_29413578-29562970.vcf.gz].sort.vcf.gz --INPUT [chr2_97489619-238903659.vcf.gz].sort.vcf.gz --INPUT [chr14_16133336-16140527.vcf.gz].sort.vcf.gz --INPUT [chr16_18486487-33214595.vcf.gz].sort.vcf.gz --INPUT [chr20_29697631-30038348.vcf.gz].sort.vcf.gz --INPUT [chrY_9055175-9057608.vcf.gz].sort.vcf.gz --INPUT [chr5_46485901-47069162.vcf.gz].sort.vcf.gz --INPUT [chr20_60001-63215.vcf.gz].sort.vcf.gz --INPUT [chr4_49708101-51743951.vcf.gz].sort.vcf.gz --INPUT [chr22_49975366-50808468.vcf.gz].sort.vcf.gz --INPUT [chr9_43236168-43263290.vcf.gz].sort.vcf.gz --INPUT [chr5_49666174-50059807.vcf.gz].sort.vcf.gz --INPUT [chrY_11013047-11016992.vcf.gz].sort.vcf.gz --INPUT [chr20_31161626-36314371.vcf.gz].sort.vcf.gz --INPUT [chr8_12284346-43983744.vcf.gz].sort.vcf.gz --INPUT [chr22_12691731-12726204.vcf.gz].sort.vcf.gz --INPUT [chr12_132224363-133265309.vcf.gz].sort.vcf.gz --INPUT [chr16_34339330-34521510.vcf.gz].sort.vcf.gz --INPUT [chr18_47019913-54536574.vcf.gz].sort.vcf.gz --INPUT [chr2_92188146-94090557.vcf.gz].sort.vcf.gz --INPUT [chr1_10001-207666.vcf.gz].sort.vcf.gz --INPUT [chr16_34580966-34584085.vcf.gz].sort.vcf.gz --INPUT [chr2_32917626-89330679.vcf.gz].sort.vcf.gz --INPUT [chr21_5010001-5166246.vcf.gz].sort.vcf.gz --INPUT [chr16_10001-18436486.vcf.gz].sort.vcf.gz --INPUT [chr11_60001-50821348.vcf.gz].sort.vcf.gz --INPUT [chrX_144475607-156030895.vcf.gz].sort.vcf.gz --INPUT [chr4_58921382-190123121.vcf.gz].sort.vcf.gz --INPUT [chr19_24891357-24898313.vcf.gz].sort.vcf.gz --INPUT [chr20_28868453-28890335.vcf.gz].sort.vcf.gz --INPUT [chr9_66591388-67920552.vcf.gz].sort.vcf.gz --INPUT [chr13_18171249-18358106.vcf.gz].sort.vcf.gz --INPUT [chr7_58169654-60828234.vcf.gz].sort.vcf.gz --INPUT [chr2_89753993-90402511.vcf.gz].sort.vcf.gz --INPUT [chr5_49609715-49611721.vcf.gz].sort.vcf.gz --INPUT [chr13_18408107-86202979.vcf.gz].sort.vcf.gz --INPUT [chr17_21814104-21984549.vcf.gz].sort.vcf.gz --INPUT [chr17_26935981-81742542.vcf.gz].sort.vcf.gz --INPUT [chr20_30456078-30761898.vcf.gz].sort.vcf.gz --INPUT [chr22_11428057-11497337.vcf.gz].sort.vcf.gz --INPUT [chr8_45927266-85664222.vcf.gz].sort.vcf.gz --INPUT [chr21_8310972-8472360.vcf.gz].sort.vcf.gz --INPUT [chr5_155761325-181478259.vcf.gz].sort.vcf.gz --INPUT [chr21_7377866-7500890.vcf.gz].sort.vcf.gz --INPUT [chr20_31051509-31107036.vcf.gz].sort.vcf.gz --INPUT [chr2_10001-16145119.vcf.gz].sort.vcf.gz --INPUT [chr2_16146120-32867130.vcf.gz].sort.vcf.gz --INPUT [chr22_16302844-16304296.vcf.gz].sort.vcf.gz --INPUT [chr1_29553836-121976459.vcf.gz].sort.vcf.gz --INPUT [chr5_50109808-139452659.vcf.gz].sort.vcf.gz -- [chr4_10001-1429358.vcf.gz].sort.vcf.gz --INPUT [chr21_8099840-8260971.vcf.gz].sort.vcf.gz --INPUT [chr9_134185537-138334717.vcf.gz].sort.vcf.gz --INPUT [chr9_63008372-63202862.vcf.gz].sort.vcf.gz --INPUT [chr8_7667128-12234345.vcf.gz].sort.vcf.gz --INPUT [chrY_56673215-56771509.vcf.gz].sort.vcf.gz --INPUT [chr21_10324328-10814560.vcf.gz].sort.vcf.gz --INPUT [chr2_91402512-92138145.vcf.gz].sort.vcf.gz --INPUT [chr11_51078349-54425074.vcf.gz].sort.vcf.gz --INPUT [chr10_38573339-38906036.vcf.gz].sort.vcf.gz --INPUT [chr1_125173584-125184587.vcf.gz].sort.vcf.gz --INPUT [chr8_85714223-145078636.vcf.gz].sort.vcf.gz --INPUT [chr6_167641394-170745979.vcf.gz].sort.vcf.gz --INPUT [chr9_10001-41225986.vcf.gz].sort.vcf.gz --INPUT [chr9_61785369-62149738.vcf.gz].sort.vcf.gz --INPUT [chr20_29413578-29562970.vcf.gz].sort.vcf.gz --INPUT [chr2_97489619-238903659.vcf.gz].sort.vcf.gz --INPUT [chr14_16133336-16140527.vcf.gz].sort.vcf.gz --INPUT [chr16_18486487-33214595.vcf.gz].sort.vcf.gz --INPUT [chr20_29697631-30038348.vcf.gz].sort.vcf.gz --INPUT [chrY_9055175-9057608.vcf.gz].sort.vcf.gz --INPUT [chr5_46485901-47069162.vcf.gz].sort.vcf.gz --INPUT [chr20_60001-63215.vcf.gz].sort.vcf.gz --INPUT [chr4_49708101-51743951.vcf.gz].sort.vcf.gz --INPUT [chr22_49975366-50808468.vcf.gz].sort.vcf.gz --INPUT [chr9_43236168-43263290.vcf.gz].sort.vcf.gz --INPUT [chr5_49666174-50059807.vcf.gz].sort.vcf.gz --INPUT [chrY_11013047-11016992.vcf.gz].sort.vcf.gz --INPUT [chr20_31161626-36314371.vcf.gz].sort.vcf.gz --INPUT [chr8_12284346-43983744.vcf.gz].sort.vcf.gz --INPUT [chr22_12691731-12726204.vcf.gz].sort.vcf.gz --INPUT [chr12_132224363-133265309.vcf.gz].sort.vcf.gz --INPUT [chr16_34339330-34521510.vcf.gz].sort.vcf.gz --INPUT [chr18_47019913-54536574.vcf.gz].sort.vcf.gz --INPUT [chr2_92188146-94090557.vcf.gz].sort.vcf.gz --INPUT [chr1_10001-207666.vcf.gz].sort.vcf.gz --INPUT [chr16_34580966-34584085.vcf.gz].sort.vcf.gz --INPUT [chr2_32917626-89330679.vcf.gz].sort.vcf.gz --INPUT [chr21_5010001-5166246.vcf.gz].sort.vcf.gz --INPUT [chr16_10001-18436486.vcf.gz].sort.vcf.gz --INPUT [chr11_60001-50821348.vcf.gz].sort.vcf.gz --INPUT [chrX_144475607-156030895.vcf.gz].sort.vcf.gz --INPUT [chr4_58921382-190123121.vcf.gz].sort.vcf.gz --INPUT [chr19_24891357-24898313.vcf.gz].sort.vcf.gz --INPUT [chr20_28868453-28890335.vcf.gz].sort.vcf.gz --INPUT [chr9_66591388-67920552.vcf.gz].sort.vcf.gz --INPUT [chr13_18171249-18358106.vcf.gz].sort.vcf.gz --INPUT [chr7_58169654-60828234.vcf.gz].sort.vcf.gz --INPUT [chr2_89753993-90402511.vcf.gz].sort.vcf.gz --INPUT [chr5_49609715-49611721.vcf.gz].sort.vcf.gz --INPUT [chr13_18408107-86202979.vcf.gz].sort.vcf.gz --INPUT [chr17_21814104-21984549.vcf.gz].sort.vcf.gz --INPUT [chr17_26935981-81742542.vcf.gz].sort.vcf.gz --INPUT [chr20_30456078-30761898.vcf.gz].sort.vcf.gz --INPUT [chr22_11428057-11497337.vcf.gz].sort.vcf.gz --INPUT [chr8_45927266-85664222.vcf.gz].sort.vcf.gz --INPUT [chr21_8310972-8472360.vcf.gz].sort.vcf.gz --INPUT [chr5_155761325-181478259.vcf.gz].sort.vcf.gz --INPUT [chr21_7377866-7500890.vcf.gz].sort.vcf.gz --INPUT [chr20_31051509-31107036.vcf.gz].sort.vcf.gz --INPUT [chr2_10001-16145119.vcf.gz].sort.vcf.gz --INPUT [chr2_16146120-32867130.vcf.gz].sort.vcf.gz --INPUT [chr22_16302844-16304296.vcf.gz].sort.vcf.gz --INPUT [chr1_29553836-121976459.vcf.gz].sort.vcf.gz --INPUT [chr5_50109808-139452659.vcf.gz].sort.vcf.gz --INPUT [chr16_34584623-36260386.vcf.gz].sort.vcf.gz --INPUT [chrY_11674124-20207793.vcf.gz].sort.vcf.gz --INPUT [chr12_34829238-37185252.vcf.gz].sort.vcf.gz --INPUT [chr4_190173122-190204555.vcf.gz].sort.vcf.gz --INPUT [chr1_13004385-16799163.vcf.gz].sort.vcf.gz --INPUT [chr5_17580549-46435900.vcf.gz].sort.vcf.gz --INPUT [chrX_114331199-115738949.vcf.gz].sort.vcf.gz --INPUT [chr1_16849164-29552233.vcf.gz].sort.vcf.gz --INPUT [chrY_56821510-56887902.vcf.gz].sort.vcf.gz --INPUT [chr20_28752591-28843401.vcf.gz].sort.vcf.gz --INPUT [chr7_143700805-159335973.vcf.gz].sort.vcf.gz --INPUT [chr20_30088349-30425128.vcf.gz].sort.vcf.gz --INPUT [chr17_22813680-26627010.vcf.gz].sort.vcf.gz --INPUT [chr15_20729747-21193490.vcf.gz].sort.vcf.gz --INPUT [chr15_17000001-19725254.vcf.gz].sort.vcf.gz --INPUT [chr6_60001-58453888.vcf.gz].sort.vcf.gz --INPUT [chr10_47870369-124121200.vcf.gz].sort.vcf.gz --INPUT [chr22_11681289-11724629.vcf.gz].sort.vcf.gz --INPUT [chr9_41229379-41237752.vcf.gz].sort.vcf.gz --INPUT [chr20_29271827-29315342.vcf.gz].sort.vcf.gz --INPUT [chr11_88002897-135076622.vcf.gz].sort.vcf.gz --INPUT [chr7_61967064-61976104.vcf.gz].sort.vcf.gz --INPUT [chr16_33264596-33392411.vcf.gz].sort.vcf.gz --INPUT [chr3_10001-90565295.vcf.gz].sort.vcf.gz --INPUT [chr18_15791048-20564714.vcf.gz].sort.vcf.gz --INPUT [chrX_37285838-49348394.vcf.gz].sort.vcf.gz --INPUT [chr3_91256422-91257890.vcf.gz].sort.vcf.gz --INPUT [chr5_139453660-155760324.vcf.gz].sort.vcf.gz --INPUT [chr17_26698999-26720420.vcf.gz].sort.vcf.gz --INPUT [chr19_60001-24448980.vcf.gz].sort.vcf.gz --INPUT [chr22_12488691-12641730.vcf.gz].sort.vcf.gz --INPUT [chr13_86252980-111703855.vcf.gz].sort.vcf.gz --INPUT [chr1_143184588-223558935.vcf.gz].sort.vcf.gz --INPUT [chr21_10269869-10274327.vcf.gz].sort.vcf.gz --INPUT [chr1_122026460-124977944.vcf.gz].sort.vcf.gz --INPUT [chr6_61371373-95020790.vcf.gz].sort.vcf.gz --INPUT [chr15_84320067-101981189.vcf.gz].sort.vcf.gz --INPUT [chr8_60001-7617127.vcf.gz].sort.vcf.gz --INPUT [chrX_58605580-62412542.vcf.gz].sort.vcf.gz --INPUT [chr10_42066266-47780368.vcf.gz].sort.vcf.gz --INPUT [chr20_26436233-26590875.vcf.gz].sort.vcf.gz --INPUT [chr5_10001-17530548.vcf.gz].sort.vcf.gz --OUTPUT joint_germline.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
  09:21:54.362 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/envs/python27/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  [Fri Feb 10 09:21:54 UTC 2023] MergeVcfs --INPUT [chr4_31832570-32833016.vcf.gz].sort.vcf.gz --INPUT [chr21_9246088-9377143.vcf.gz].sort.vcf.gz --INPUT [chr9_63968448-64135013.vcf.gz].sort.vcf.gz --INPUT [chr18_10001-15410899.vcf.gz].sort.vcf.gz --INPUT [chr21_5443559-5449012.vcf.gz].sort.vcf.gz --INPUT [chr6_95070791-167591393.vcf.gz].sort.vcf.gz --INPUT [chr22_10834644-10874572.vcf.gz].sort.vcf.gz --INPUT [chr22_18339130-18433513.vcf.gz].sort.vcf.gz --INPUT [chr21_12965809-43212462.vcf.gz].sort.vcf.gz --INPUT [chr10_39230137-39409792.vcf.gz].sort.vcf.gz --INPUT [chr4_49486925-49658100.vcf.gz].sort.vcf.gz --INPUT [chr22_12275589-12438690.vcf.gz].sort.vcf.gz --INPUT [chr16_46380683-90228345.vcf.gz].sort.vcf.gz --INPUT [chr22_11118988-11160921.vcf.gz].sort.vcf.gz --INPUT [chr1_228608365-248946422.vcf.gz].sort.vcf.gz --INPUT [chrY_10682443-10691573.vcf.gz].sort.vcf.gz --INPUT [chr4_8816478-9272916.vcf.gz].sort.vcf.gz --INPUT [chr3_90568829-90722458.vcf.gz].sort.vcf.gz --INPUT [chr21_43262463-46699983.vcf.gz].sort.vcf.gz --INPUT [chr18_54537529-80263285.vcf.gz].sort.vcf.gz --INPUT [chr11_71055697-87978202.vcf.gz].sort.vcf.gz --INPUT [chr10_124121503-133690466.vcf.gz].sort.vcf.gz --INPUT [chr17_491112-21795850.vcf.gz].sort.vcf.gz --INPUT [chr13_111843442-113673020.vcf.gz].sort.vcf.gz --INPUT [chr12_10001-7083650.vcf.gz].sort.vcf.gz --INPUT [chr12_7084651-34719407.vcf.gz].sort.vcf.gz --INPUT [chr4_10001-1429358.vcf.gz].sort.vcf.gz --INPUT [chr21_8099840-8260971.vcf.gz].sort.vcf.gz --INPUT [chr9_134185537-138334717.vcf.gz].sort.vcf.gz --INPUT [chr9_63008372-63202862.vcf.gz].sort.vcf.gz --INPUT [chr8_7667128-12234345.vcf.gz].sort.vcf.gz --INPUT [chrY_56673215-56771509.vcf.gz].sort.vcf.gz --INPUT [chr21_10324328-10814560.vcf.gz].sort.vcf.gz --INPUT [chr2_91402512-92138145.vcf.gz].sort.vcf.gz --INPUT [chr11_51078349-54425074.vcf.gz].sort.vcf.gz --INPUT [chr10_38573339-38906036.vcf.gz].sort.vcf.gz --INPUT [chr1_125173584-125184587.vcf.gz].sort.vcf.gz --INPUT [chr8_85714223-145078636.vcf.gz].sort.vcf.gz --INPUT [chr6_167641394-170745979.vcf.gz].sort.vcf.gz --INPUT [chr9_10001-41225986.vcf.gz].sort.vcf.gz --INPUT [chr9_61785369-62149738.vcf.gz].sort.vcf.gz --INPUT [chr20_29413578-29562970.vcf.gz].sort.vcf.gz --INPUT [chr2_97489619-238903659.vcf.gz].sort.vcf.gz --INPUT [chr14_16133336-16140527.vcf.gz].sort.vcf.gz --INPUT [chr16_18486487-33214595.vcf.gz].sort.vcf.gz --INPUT [chr20_29697631-30038348.vcf.gz].sort.vcf.gz --INPUT [chrY_9055175-9057608.vcf.gz].sort.vcf.gz --INPUT [chr5_46485901-47069162.vcf.gz].sort.vcf.gz --INPUT [chr20_60001-63215.vcf.gz].sort.vcf.gz --INPUT [chr4_49708101-51743951.vcf.gz].sort.vcf.gz --INPUT [chr22_49975366-50808468.vcf.gz].sort.vcf.gz --INPUT [chr9_43236168-43263290.vcf.gz].sort.vcf.gz --INPUT [chr5_49666174-50059807.vcf.gz].sort.vcf.gz --INPUT [chrY_11013047-11016992.vcf.gz].sort.vcf.gz --INPUT [chr20_31161626-36314371.vcf.gz].sort.vcf.gz --INPUT [chr8_12284346-43983744.vcf.gz].sort.vcf.gz --INPUT [chr22_12691731-12726204.vcf.gz].sort.vcf.gz --INPUT [chr12_132224363-133265309.vcf.gz].sort.vcf.gz --INPUT [chr16_34339330-34521510.vcf.gz].sort.vcf.gz --INPUT [chr18_47019913-54536574.vcf.gz].sort.vcf.gz --INPUT [chr2_92188146-94090557.vcf.gz].sort.vcf.gz --INPUT [chr1_10001-207666.vcf.gz].sort.vcf.gz --INPUT [chr16_34580966-34584085.vcf.gz].sort.vcf.gz --INPUT [chr2_32917626-89330679.vcf.gz].sort.vcf.gz --INPUT [chr21_5010001-5166246.vcf.gz].sort.vcf.gz --INPUT [chr16_10001-18436486.vcf.gz].sort.vcf.gz --INPUT [chr11_60001-50821348.vcf.gz].sort.vcf.gz --INPUT [chrX_144475607-156030895.vcf.gz].sort.vcf.gz --INPUT [chr4_58921382-190123121.vcf.gz].sort.vcf.gz --INPUT [chr19_24891357-24898313.vcf.gz].sort.vcf.gz --INPUT [chr20_28868453-28890335.vcf.gz].sort.vcf.gz --INPUT [chr9_66591388-67920552.vcf.gz].sort.vcf.gz --INPUT [chr13_18171249-18358106.vcf.gz].sort.vcf.gz --INPUT [chr7_58169654-60828234.vcf.gz].sort.vcf.gz --INPUT [chr2_89753993-90402511.vcf.gz].sort.vcf.gz --INPUT [chr5_49609715-49611721.vcf.gz].sort.vcf.gz --INPUT [chr13_18408107-86202979.vcf.gz].sort.vcf.gz --INPUT [chr17_21814104-21984549.vcf.gz].sort.vcf.gz --INPUT [chr17_26935981-81742542.vcf.gz].sort.vcf.gz --INPUT [chr20_30456078-30761898.vcf.gz].sort.vcf.gz --INPUT [chr22_11428057-11497337.vcf.gz].sort.vcf.gz --INPUT [chr8_45927266-85664222.vcf.gz].sort.vcf.gz --INPUT [chr21_8310972-8472360.vcf.gz].sort.vcf.gz --INPUT [chr5_155761325-181478259.vcf.gz].sort.vcf.gz --INPUT [chr21_7377866-7500890.vcf.gz].sort.vcf.gz --INPUT [chr20_31051509-31107036.vcf.gz].sort.vcf.gz --INPUT [chr2_10001-16145119.vcf.gz].sort.vcf.gz --INPUT [chr2_16146120-32867130.vcf.gz].sort.vcf.gz --INPUT [chr22_16302844-16304296.vcf.gz].sort.vcf.gz --INPUT [chr1_29553836-121976459.vcf.gz].sort.vcf.gz --INPUT [chr5_50109808-139452659.vcf.gz].sort.vcf.gz --INPUT [chr16_34584623-36260386.vcf.gz].sort.vcf.gz --INPUT [chrY_11674124-20207793.vcf.gz].sort.vcf.gz --INPUT [chr12_34829238-37185252.vcf.gz].sort.vcf.gz --INPUT [chr4_190173122-190204555.vcf.gz].sort.vcf.gz --INPUT [chr1_13004385-16799163.vcf.gz].sort.vcf.gz --INPUT [chr5_17580549-46435900.vcf.gz].sort.vcf.gz --INPUT [chrX_114331199-115738949.vcf.gz].sort.vcf.gz --INPUT [chr1_16849164-29552233.vcf.gz].sort.vcf.gz --INPUT [chrY_56821510-56887902.vcf.gz].sort.vcf.gz --INPUT [chr20_28752591-28843401.vcf.gz].sort.vcf.gz --INPUT [chr7_143700805-159335973.vcf.gz].sort.vcf.gz --INPUT [chr20_30088349-30425128.vcf.gz].sort.vcf.gz --INPUT [chr17_22813680-26627010.vcf.gz].sort.vcf.gz --INPUT [chr15_20729747-21193490.vcf.gz].sort.vcf.gz --INPUT [chr15_17000001-19725254.vcf.gz].sort.vcf.gz --INPUT [chr6_60001-58453888.vcf.gz].sort.vcf.gz --INPUT [chr10_47870369-124121200.vcf.gz].sort.vcf.gz --INPUT [chr22_11681289-11724629.vcf.gz].sort.vcf.gz --INPUT [chr9_41229379-41237752.vcf.gz].sort.vcf.gz --INPUT [chr20_29271827-29315342.vcf.gz].sort.vcf.gz --INPUT [chr11_88002897-135076622.vcf.gz].sort.vcf.gz --INPUT [chr7_61967064-61976104.vcf.gz].sort.vcf.gz --INPUT [chr16_33264596-33392411.vcf.gz].sort.vcf.gz --INPUT [chr3_10001-90565295.vcf.gz].sort.vcf.gz --INPUT [chr18_15791048-20564714.vcf.gz].sort.vcf.gz --INPUT [chrX_37285838-49348394.vcf.gz].sort.vcf.gz --INPUT [chr3_91256422-91257890.vcf.gz].sort.vcf.gz --INPUT [chr5_139453660-155760324.vcf.gz].sort.vcf.gz --INPUT [chr17_26698999-26720420.vcf.gz].sort.vcf.gz --INPUT [chr19_60001-24448980.vcf.gz].sort.vcf.gz --INPUT [chr22_12488691-12641730.vcf.gz].sort.vcf.gz --INPUT [chr13_86252980-111703855.vcf.gz].sort.vcf.gz --INPUT [chr1_143184588-223558935.vcf.gz].sort.vcf.gz --INPUT [chr21_10269869-10274327.vcf.gz].sort.vcf.gz --INPUT [chr1_122026460-124977944.vcf.gz].sort.vcf.gz --INPUT [chr6_61371373-95020790.vcf.gz].sort.vcf.gz --INPUT [chr15_84320067-101981189.vcf.gz].sort.vcf.gz --INPUT [chr8_60001-7617127.vcf.gz].sort.vcf.gz --INPUT [chrX_58605580-62412542.vcf.gz].sort.vcf.gz --INPUT [chr10_42066266-47780368.vcf.gz].sort.vcf.gz --INPUT [chr20_26436233-26590875.vcf.gz].sort.vcf.gz --INPUT [chr5_10001-17530548.vcf.gz].sort.vcf.gz --OUTPUT joint_germline.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR . --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX true --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
  [Fri Feb 10 09:22:04 UTC 2023] Executing as root@26047e876e98 on Linux 3.10.0-862.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.13+7-b1751.21; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.3.0.0
  [Fri Feb 10 09:22:04 UTC 2023] picard.vcf.MergeVcfs done. Elapsed time: 0.18 minutes.
  Runtime.totalMemory()=2147483648
  To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
  htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Not in GZIP format, for input source: file://%5Bchr4_31832570-32833016.vcf.gz%5D.sort.vcf.gz
  	at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:264)
  	at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:103)
  	at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:128)
  	at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)
  	at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:81)
  	at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:145)
  	at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:182)
  	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:309)
  	at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
  	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
  	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
  	at org.broadinstitute.hellbender.Main.main(Main.java:289)
  Caused by: java.util.zip.ZipException: Not in GZIP format
  	at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:166)
  	at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:80)
  	at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:92)
  	at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:258)
  	... 11 more

Relevant files

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System information

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@nagihayate nagihayate added the bug Something isn't working label Feb 11, 2023
@FriederikeHanssen
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Hi! To help you could you sent us:

  1. The Nextflow command you used to launch the pipeline
  2. Any custom Nextflow config files
  3. The corresponding .nextflow.log file, where you are running the analysis.
    ?

@nagihayate
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Hi, thanks your reply!

  1. nextflow run nf-core/sarek --input input.csv --outdir -w work --wes --igenomes_base igenomes -r 3.0.1 --tools mutect2,haplotypecaller --joint_germline .
  2. None.
  3. The contents of the corresponding .nextflow.log file is described above.

Description of the bug

When i adding paramaters(--tools mutect2,haplotypecaller --joint_germline) to the process, there is an error in "MERGE_GENOTYPEGVCFS (joint_variant_calling)". And i can't found the right place to fix this problem.

Command used and terminal output

Pipeline completed with errors-
Error executing process > 'NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS (joint_variant_calling)'

Caused by:
  Process `NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS (joint_variant_calling)` terminated with an error exit status (3)

Command executed:

  gatk --java-options "-Xmx36g" MergeVcfs \
      --INPUT [chr4_31832570-32833016.vcf.gz].sort.vcf.gz --INPUT [chr21_9246088-9377143.vcf.gz].sort.vcf.gz --INPUT [chr9_63968448-64135013.vcf.gz].sort.vcf.gz --INPUT [chr18_10001-15410899.vcf.gz].sort.vcf.gz --INPUT [chr21_5443559-5449012.vcf.gz].sort.vcf.gz --INPUT [chr6_95070791-167591393.vcf.gz].sort.vcf.gz --INPUT [chr22_10834644-10874572.vcf.gz].sort.vcf.gz --INPUT [chr22_18339130-18433513.vcf.gz].sort.vcf.gz --INPUT [chr21_12965809-43212462.vcf.gz].sort.vcf.gz --INPUT [chr10_39230137-39409792.vcf.gz].sort.vcf.gz --INPUT [chr4_49486925-49658100.vcf.gz].sort.vcf.gz --INPUT [chr22_12275589-12438690.vcf.gz].sort.vcf.gz --INPUT [chr16_46380683-90228345.vcf.gz].sort.vcf.gz --INPUT [chr22_11118988-11160921.vcf.gz].sort.vcf.gz --INPUT [chr1_228608365-248946422.vcf.gz].sort.vcf.gz --INPUT [chrY_10682443-10691573.vcf.gz].sort.vcf.gz --INPUT [chr4_8816478-9272916.vcf.gz].sort.vcf.gz --INPUT [chr3_90568829-90722458.vcf.gz].sort.vcf.gz --INPUT [chr21_43262463-46699983.vcf.gz].sort.vcf.gz --INPUT [chr18_54537529-80263285.vcf.gz].sort.vcf.gz --INPUT [chr11_71055697-87978202.vcf.gz].sort.vcf.gz --INPUT [chr10_124121503-133690466.vcf.gz].sort.vcf.gz --INPUT [chr17_491112-21795850.vcf.gz].sort.vcf.gz --INPUT [chr13_111843442-113673020.vcf.gz].sort.vcf.gz --INPUT [chr12_10001-7083650.vcf.gz].sort.vcf.gz --INPUT [chr12_7084651-34719407.vcf.gz].sort.vcf.gz --INPUT [chr4_10001-1429358.vcf.gz].sort.vcf.gz --INPUT [chr21_8099840-8260971.vcf.gz].sort.vcf.gz --INPUT [chr9_134185537-138334717.vcf.gz].sort.vcf.gz --INPUT [chr9_63008372-63202862.vcf.gz].sort.vcf.gz --INPUT [chr8_7667128-12234345.vcf.gz].sort.vcf.gz --INPUT [chrY_56673215-56771509.vcf.gz].sort.vcf.gz --INPUT [chr21_10324328-10814560.vcf.gz].sort.vcf.gz --INPUT [chr2_91402512-92138145.vcf.gz].sort.vcf.gz --INPUT [chr11_51078349-54425074.vcf.gz].sort.vcf.gz --INPUT [chr10_38573339-38906036.vcf.gz].sort.vcf.gz --INPUT [chr1_125173584-125184587.vcf.gz].sort.vcf.gz --INPUT [chr8_85714223-145078636.vcf.gz].sort.vcf.gz --INPUT [chr6_167641394-170745979.vcf.gz].sort.vcf.gz --INPUT [chr9_10001-41225986.vcf.gz].sort.vcf.gz --INPUT [chr9_61785369-62149738.vcf.gz].sort.vcf.gz --INPUT [chr20_29413578-29562970.vcf.gz].sort.vcf.gz --INPUT [chr2_97489619-238903659.vcf.gz].sort.vcf.gz --INPUT [chr14_16133336-16140527.vcf.gz].sort.vcf.gz --INPUT [chr16_18486487-33214595.vcf.gz].sort.vcf.gz --INPUT [chr20_29697631-30038348.vcf.gz].sort.vcf.gz --INPUT [chrY_9055175-9057608.vcf.gz].sort.vcf.gz --INPUT [chr5_46485901-47069162.vcf.gz].sort.vcf.gz --INPUT [chr20_60001-63215.vcf.gz].sort.vcf.gz --INPUT [chr4_49708101-51743951.vcf.gz].sort.vcf.gz --INPUT [chr22_49975366-50808468.vcf.gz].sort.vcf.gz --INPUT [chr9_43236168-43263290.vcf.gz].sort.vcf.gz --INPUT [chr5_49666174-50059807.vcf.gz].sort.vcf.gz --INPUT [chrY_11013047-11016992.vcf.gz].sort.vcf.gz --INPUT [chr20_31161626-36314371.vcf.gz].sort.vcf.gz --INPUT [chr8_12284346-43983744.vcf.gz].sort.vcf.gz --INPUT [chr22_12691731-12726204.vcf.gz].sort.vcf.gz --INPUT [chr12_132224363-133265309.vcf.gz].sort.vcf.gz --INPUT [chr16_34339330-34521510.vcf.gz].sort.vcf.gz --INPUT [chr18_47019913-54536574.vcf.gz].sort.vcf.gz --INPUT [chr2_92188146-94090557.vcf.gz].sort.vcf.gz --INPUT [chr1_10001-207666.vcf.gz].sort.vcf.gz --INPUT [chr16_34580966-34584085.vcf.gz].sort.vcf.gz --INPUT [chr2_32917626-89330679.vcf.gz].sort.vcf.gz --INPUT [chr21_5010001-5166246.vcf.gz].sort.vcf.gz --INPUT [chr16_10001-18436486.vcf.gz].sort.vcf.gz --INPUT [chr11_60001-50821348.vcf.gz].sort.vcf.gz --INPUT [chrX_144475607-156030895.vcf.gz].sort.vcf.gz --INPUT [chr4_58921382-190123121.vcf.gz].sort.vcf.gz --INPUT [chr19_24891357-24898313.vcf.gz].sort.vcf.gz --INPUT [chr20_28868453-28890335.vcf.gz].sort.vcf.gz --INPUT [chr9_66591388-67920552.vcf.gz].sort.vcf.gz --INPUT [chr13_18171249-18358106.vcf.gz].sort.vcf.gz --INPUT [chr7_58169654-60828234.vcf.gz].sort.vcf.gz --INPUT [chr2_89753993-90402511.vcf.gz].sort.vcf.gz --INPUT [chr5_49609715-49611721.vcf.gz].sort.vcf.gz --INPUT [chr13_18408107-86202979.vcf.gz].sort.vcf.gz --INPUT [chr17_21814104-21984549.vcf.gz].sort.vcf.gz --INPUT [chr17_26935981-81742542.vcf.gz].sort.vcf.gz --INPUT [chr20_30456078-30761898.vcf.gz].sort.vcf.gz --INPUT [chr22_11428057-11497337.vcf.gz].sort.vcf.gz --INPUT [chr8_45927266-85664222.vcf.gz].sort.vcf.gz --INPUT [chr21_8310972-8472360.vcf.gz].sort.vcf.gz --INPUT [chr5_155761325-181478259.vcf.gz].sort.vcf.gz --INPUT [chr21_7377866-7500890.vcf.gz].sort.vcf.gz --INPUT [chr20_31051509-31107036.vcf.gz].sort.vcf.gz --INPUT [chr2_10001-16145119.vcf.gz].sort.vcf.gz --INPUT [chr2_16146120-32867130.vcf.gz].sort.vcf.gz --INPUT [chr22_16302844-16304296.vcf.gz].sort.vcf.gz --INPUT [chr1_29553836-121976459.vcf.gz].sort.vcf.gz --INPUT [chr5_50109808-139452659.vcf.gz].sort.vcf.gz --INPUT [chr16_34584623-36260386.vcf.gz].sort.vcf.gz --INPUT [chrY_11674124-20207793.vcf.gz].sort.vcf.gz --INPUT [chr12_34829238-37185252.vcf.gz].sort.vcf.gz --INPUT [chr4_190173122-190204555.vcf.gz].sort.vcf.gz --INPUT [chr1_13004385-16799163.vcf.gz].sort.vcf.gz --INPUT [chr5_17580549-46435900.vcf.gz].sort.vcf.gz --INPUT [chrX_114331199-115738949.vcf.gz].sort.vcf.gz --INPUT [chr1_16849164-29552233.vcf.gz].sort.vcf.gz --INPUT [chrY_56821510-56887902.vcf.gz].sort.vcf.gz --INPUT [chr20_28752591-28843401.vcf.gz].sort.vcf.gz --INPUT [chr7_143700805-159335973.vcf.gz].sort.vcf.gz --INPUT [chr20_30088349-30425128.vcf.gz].sort.vcf.gz --INPUT [chr17_22813680-26627010.vcf.gz].sort.vcf.gz --INPUT [chr15_20729747-21193490.vcf.gz].sort.vcf.gz --INPUT [chr15_17000001-19725254.vcf.gz].sort.vcf.gz --INPUT [chr6_60001-58453888.vcf.gz].sort.vcf.gz --INPUT [chr10_47870369-124121200.vcf.gz].sort.vcf.gz --INPUT [chr22_11681289-11724629.vcf.gz].sort.vcf.gz --INPUT [chr9_41229379-41237752.vcf.gz].sort.vcf.gz --INPUT [chr20_29271827-29315342.vcf.gz].sort.vcf.gz --INPUT [chr11_88002897-135076622.vcf.gz].sort.vcf.gz --INPUT [chr7_61967064-61976104.vcf.gz].sort.vcf.gz --INPUT [chr16_33264596-33392411.vcf.gz].sort.vcf.gz --INPUT [chr3_10001-90565295.vcf.gz].sort.vcf.gz --INPUT [chr18_15791048-20564714.vcf.gz].sort.vcf.gz --INPUT [chrX_37285838-49348394.vcf.gz].sort.vcf.gz --INPUT [chr3_91256422-91257890.vcf.gz].sort.vcf.gz --INPUT [chr5_139453660-155760324.vcf.gz].sort.vcf.gz --INPUT [chr17_26698999-26720420.vcf.gz].sort.vcf.gz --INPUT [chr19_60001-24448980.vcf.gz].sort.vcf.gz --INPUT [chr22_12488691-12641730.vcf.gz].sort.vcf.gz --INPUT [chr13_86252980-111703855.vcf.gz].sort.vcf.gz --INPUT [chr1_143184588-223558935.vcf.gz].sort.vcf.gz --INPUT [chr21_10269869-10274327.vcf.gz].sort.vcf.gz --INPUT [chr1_122026460-124977944.vcf.gz].sort.vcf.gz --INPUT [chr6_61371373-95020790.vcf.gz].sort.vcf.gz --INPUT [chr15_84320067-101981189.vcf.gz].sort.vcf.gz --INPUT [chr8_60001-7617127.vcf.gz].sort.vcf.gz --INPUT [chrX_58605580-62412542.vcf.gz].sort.vcf.gz --INPUT [chr10_42066266-47780368.vcf.gz].sort.vcf.gz --INPUT [chr20_26436233-26590875.vcf.gz].sort.vcf.gz --INPUT [chr5_10001-17530548.vcf.gz].sort.vcf.gz \
      --OUTPUT joint_germline.vcf.gz \
      --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict \
      --TMP_DIR . \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:MERGE_GENOTYPEGVCFS":
      gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
  END_VERSIONS

Command exit status:
  3

Command output:
  (empty)

Command error:
  Using GATK jar /opt/conda/envs/python27/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-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 -Xmx36g -jar /opt/conda/envs/python27/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar MergeVcfs --INPUT [chr4_31832570-32833016.vcf.gz].sort.vcf.gz --INPUT [chr21_9246088-9377143.vcf.gz].sort.vcf.gz --INPUT [chr9_63968448-64135013.vcf.gz].sort.vcf.gz --INPUT [chr18_10001-15410899.vcf.gz].sort.vcf.gz --INPUT [chr21_5443559-5449012.vcf.gz].sort.vcf.gz --INPUT [chr6_95070791-167591393.vcf.gz].sort.vcf.gz --INPUT [chr22_10834644-10874572.vcf.gz].sort.vcf.gz --INPUT [chr22_18339130-18433513.vcf.gz].sort.vcf.gz --INPUT [chr21_12965809-43212462.vcf.gz].sort.vcf.gz --INPUT [chr10_39230137-39409792.vcf.gz].sort.vcf.gz --INPUT [chr4_49486925-49658100.vcf.gz].sort.vcf.gz --INPUT [chr22_12275589-12438690.vcf.gz].sort.vcf.gz --INPUT [chr16_46380683-90228345.vcf.gz].sort.vcf.gz --INPUT [chr22_11118988-11160921.vcf.gz].sort.vcf.gz --INPUT [chr1_228608365-248946422.vcf.gz].sort.vcf.gz --INPUT [chrY_10682443-10691573.vcf.gz].sort.vcf.gz --INPUT [chr4_8816478-9272916.vcf.gz].sort.vcf.gz --INPUT [chr3_90568829-90722458.vcf.gz].sort.vcf.gz --INPUT [chr21_43262463-46699983.vcf.gz].sort.vcf.gz --INPUT [chr18_54537529-80263285.vcf.gz].sort.vcf.gz --INPUT [chr11_71055697-87978202.vcf.gz].sort.vcf.gz --INPUT [chr10_124121503-133690466.vcf.gz].sort.vcf.gz --INPUT [chr17_491112-21795850.vcf.gz].sort.vcf.gz --INPUT [chr13_111843442-113673020.vcf.gz].sort.vcf.gz --INPUT [chr12_10001-7083650.vcf.gz].sort.vcf.gz --INPUT [chr12_7084651-34719407.vcf.gz].sort.vcf.gz --INPUT [chr4_10001-1429358.vcf.gz].sort.vcf.gz --INPUT [chr21_8099840-8260971.vcf.gz].sort.vcf.gz --INPUT [chr9_134185537-138334717.vcf.gz].sort.vcf.gz --INPUT [chr9_63008372-63202862.vcf.gz].sort.vcf.gz --INPUT [chr8_7667128-12234345.vcf.gz].sort.vcf.gz --INPUT [chrY_56673215-56771509.vcf.gz].sort.vcf.gz --INPUT [chr21_10324328-10814560.vcf.gz].sort.vcf.gz --INPUT [chr2_91402512-92138145.vcf.gz].sort.vcf.gz --INPUT [chr11_51078349-54425074.vcf.gz].sort.vcf.gz --INPUT [chr10_38573339-38906036.vcf.gz].sort.vcf.gz --INPUT [chr1_125173584-125184587.vcf.gz].sort.vcf.gz --INPUT [chr8_85714223-145078636.vcf.gz].sort.vcf.gz --INPUT [chr6_167641394-170745979.vcf.gz].sort.vcf.gz --INPUT [chr9_10001-41225986.vcf.gz].sort.vcf.gz --INPUT [chr9_61785369-62149738.vcf.gz].sort.vcf.gz --INPUT [chr20_29413578-29562970.vcf.gz].sort.vcf.gz --INPUT [chr2_97489619-238903659.vcf.gz].sort.vcf.gz --INPUT [chr14_16133336-16140527.vcf.gz].sort.vcf.gz --INPUT [chr16_18486487-33214595.vcf.gz].sort.vcf.gz --INPUT [chr20_29697631-30038348.vcf.gz].sort.vcf.gz --INPUT [chrY_9055175-9057608.vcf.gz].sort.vcf.gz --INPUT [chr5_46485901-47069162.vcf.gz].sort.vcf.gz --INPUT [chr20_60001-63215.vcf.gz].sort.vcf.gz --INPUT [chr4_49708101-51743951.vcf.gz].sort.vcf.gz --INPUT [chr22_49975366-50808468.vcf.gz].sort.vcf.gz --INPUT [chr9_43236168-43263290.vcf.gz].sort.vcf.gz --INPUT [chr5_49666174-50059807.vcf.gz].sort.vcf.gz --INPUT [chrY_11013047-11016992.vcf.gz].sort.vcf.gz --INPUT [chr20_31161626-36314371.vcf.gz].sort.vcf.gz --INPUT [chr8_12284346-43983744.vcf.gz].sort.vcf.gz --INPUT [chr22_12691731-12726204.vcf.gz].sort.vcf.gz --INPUT [chr12_132224363-133265309.vcf.gz].sort.vcf.gz --INPUT [chr16_34339330-34521510.vcf.gz].sort.vcf.gz --INPUT [chr18_47019913-54536574.vcf.gz].sort.vcf.gz --INPUT [chr2_92188146-94090557.vcf.gz].sort.vcf.gz --INPUT [chr1_10001-207666.vcf.gz].sort.vcf.gz --INPUT [chr16_34580966-34584085.vcf.gz].sort.vcf.gz --INPUT [chr2_32917626-89330679.vcf.gz].sort.vcf.gz --INPUT [chr21_5010001-5166246.vcf.gz].sort.vcf.gz --INPUT [chr16_10001-18436486.vcf.gz].sort.vcf.gz --INPUT [chr11_60001-50821348.vcf.gz].sort.vcf.gz --INPUT [chrX_144475607-156030895.vcf.gz].sort.vcf.gz --INPUT [chr4_58921382-190123121.vcf.gz].sort.vcf.gz --INPUT [chr19_24891357-24898313.vcf.gz].sort.vcf.gz --INPUT [chr20_28868453-28890335.vcf.gz].sort.vcf.gz --INPUT [chr9_66591388-67920552.vcf.gz].sort.vcf.gz --INPUT [chr13_18171249-18358106.vcf.gz].sort.vcf.gz --INPUT [chr7_58169654-60828234.vcf.gz].sort.vcf.gz --INPUT [chr2_89753993-90402511.vcf.gz].sort.vcf.gz --INPUT [chr5_49609715-49611721.vcf.gz].sort.vcf.gz --INPUT [chr13_18408107-86202979.vcf.gz].sort.vcf.gz --INPUT [chr17_21814104-21984549.vcf.gz].sort.vcf.gz --INPUT [chr17_26935981-81742542.vcf.gz].sort.vcf.gz --INPUT [chr20_30456078-30761898.vcf.gz].sort.vcf.gz --INPUT [chr22_11428057-11497337.vcf.gz].sort.vcf.gz --INPUT [chr8_45927266-85664222.vcf.gz].sort.vcf.gz --INPUT [chr21_8310972-8472360.vcf.gz].sort.vcf.gz --INPUT [chr5_155761325-181478259.vcf.gz].sort.vcf.gz --INPUT [chr21_7377866-7500890.vcf.gz].sort.vcf.gz --INPUT [chr20_31051509-31107036.vcf.gz].sort.vcf.gz --INPUT [chr2_10001-16145119.vcf.gz].sort.vcf.gz --INPUT [chr2_16146120-32867130.vcf.gz].sort.vcf.gz --INPUT [chr22_16302844-16304296.vcf.gz].sort.vcf.gz --INPUT [chr1_29553836-121976459.vcf.gz].sort.vcf.gz --INPUT [chr5_50109808-139452659.vcf.gz].sort.vcf.gz -- [chr4_10001-1429358.vcf.gz].sort.vcf.gz --INPUT [chr21_8099840-8260971.vcf.gz].sort.vcf.gz --INPUT [chr9_134185537-138334717.vcf.gz].sort.vcf.gz --INPUT [chr9_63008372-63202862.vcf.gz].sort.vcf.gz --INPUT [chr8_7667128-12234345.vcf.gz].sort.vcf.gz --INPUT [chrY_56673215-56771509.vcf.gz].sort.vcf.gz --INPUT [chr21_10324328-10814560.vcf.gz].sort.vcf.gz --INPUT [chr2_91402512-92138145.vcf.gz].sort.vcf.gz --INPUT [chr11_51078349-54425074.vcf.gz].sort.vcf.gz --INPUT [chr10_38573339-38906036.vcf.gz].sort.vcf.gz --INPUT [chr1_125173584-125184587.vcf.gz].sort.vcf.gz --INPUT [chr8_85714223-145078636.vcf.gz].sort.vcf.gz --INPUT [chr6_167641394-170745979.vcf.gz].sort.vcf.gz --INPUT [chr9_10001-41225986.vcf.gz].sort.vcf.gz --INPUT [chr9_61785369-62149738.vcf.gz].sort.vcf.gz --INPUT [chr20_29413578-29562970.vcf.gz].sort.vcf.gz --INPUT [chr2_97489619-238903659.vcf.gz].sort.vcf.gz --INPUT [chr14_16133336-16140527.vcf.gz].sort.vcf.gz --INPUT [chr16_18486487-33214595.vcf.gz].sort.vcf.gz --INPUT [chr20_29697631-30038348.vcf.gz].sort.vcf.gz --INPUT [chrY_9055175-9057608.vcf.gz].sort.vcf.gz --INPUT [chr5_46485901-47069162.vcf.gz].sort.vcf.gz --INPUT [chr20_60001-63215.vcf.gz].sort.vcf.gz --INPUT [chr4_49708101-51743951.vcf.gz].sort.vcf.gz --INPUT [chr22_49975366-50808468.vcf.gz].sort.vcf.gz --INPUT [chr9_43236168-43263290.vcf.gz].sort.vcf.gz --INPUT [chr5_49666174-50059807.vcf.gz].sort.vcf.gz --INPUT [chrY_11013047-11016992.vcf.gz].sort.vcf.gz --INPUT [chr20_31161626-36314371.vcf.gz].sort.vcf.gz --INPUT [chr8_12284346-43983744.vcf.gz].sort.vcf.gz --INPUT [chr22_12691731-12726204.vcf.gz].sort.vcf.gz --INPUT [chr12_132224363-133265309.vcf.gz].sort.vcf.gz --INPUT [chr16_34339330-34521510.vcf.gz].sort.vcf.gz --INPUT [chr18_47019913-54536574.vcf.gz].sort.vcf.gz --INPUT [chr2_92188146-94090557.vcf.gz].sort.vcf.gz --INPUT [chr1_10001-207666.vcf.gz].sort.vcf.gz --INPUT [chr16_34580966-34584085.vcf.gz].sort.vcf.gz --INPUT [chr2_32917626-89330679.vcf.gz].sort.vcf.gz --INPUT [chr21_5010001-5166246.vcf.gz].sort.vcf.gz --INPUT [chr16_10001-18436486.vcf.gz].sort.vcf.gz --INPUT [chr11_60001-50821348.vcf.gz].sort.vcf.gz --INPUT [chrX_144475607-156030895.vcf.gz].sort.vcf.gz --INPUT [chr4_58921382-190123121.vcf.gz].sort.vcf.gz --INPUT [chr19_24891357-24898313.vcf.gz].sort.vcf.gz --INPUT [chr20_28868453-28890335.vcf.gz].sort.vcf.gz --INPUT [chr9_66591388-67920552.vcf.gz].sort.vcf.gz --INPUT [chr13_18171249-18358106.vcf.gz].sort.vcf.gz --INPUT [chr7_58169654-60828234.vcf.gz].sort.vcf.gz --INPUT [chr2_89753993-90402511.vcf.gz].sort.vcf.gz --INPUT [chr5_49609715-49611721.vcf.gz].sort.vcf.gz --INPUT [chr13_18408107-86202979.vcf.gz].sort.vcf.gz --INPUT [chr17_21814104-21984549.vcf.gz].sort.vcf.gz --INPUT [chr17_26935981-81742542.vcf.gz].sort.vcf.gz --INPUT [chr20_30456078-30761898.vcf.gz].sort.vcf.gz --INPUT [chr22_11428057-11497337.vcf.gz].sort.vcf.gz --INPUT [chr8_45927266-85664222.vcf.gz].sort.vcf.gz --INPUT [chr21_8310972-8472360.vcf.gz].sort.vcf.gz --INPUT [chr5_155761325-181478259.vcf.gz].sort.vcf.gz --INPUT [chr21_7377866-7500890.vcf.gz].sort.vcf.gz --INPUT [chr20_31051509-31107036.vcf.gz].sort.vcf.gz --INPUT [chr2_10001-16145119.vcf.gz].sort.vcf.gz --INPUT [chr2_16146120-32867130.vcf.gz].sort.vcf.gz --INPUT [chr22_16302844-16304296.vcf.gz].sort.vcf.gz --INPUT [chr1_29553836-121976459.vcf.gz].sort.vcf.gz --INPUT [chr5_50109808-139452659.vcf.gz].sort.vcf.gz --INPUT [chr16_34584623-36260386.vcf.gz].sort.vcf.gz --INPUT [chrY_11674124-20207793.vcf.gz].sort.vcf.gz --INPUT [chr12_34829238-37185252.vcf.gz].sort.vcf.gz --INPUT [chr4_190173122-190204555.vcf.gz].sort.vcf.gz --INPUT [chr1_13004385-16799163.vcf.gz].sort.vcf.gz --INPUT [chr5_17580549-46435900.vcf.gz].sort.vcf.gz --INPUT [chrX_114331199-115738949.vcf.gz].sort.vcf.gz --INPUT [chr1_16849164-29552233.vcf.gz].sort.vcf.gz --INPUT [chrY_56821510-56887902.vcf.gz].sort.vcf.gz --INPUT [chr20_28752591-28843401.vcf.gz].sort.vcf.gz --INPUT [chr7_143700805-159335973.vcf.gz].sort.vcf.gz --INPUT [chr20_30088349-30425128.vcf.gz].sort.vcf.gz --INPUT [chr17_22813680-26627010.vcf.gz].sort.vcf.gz --INPUT [chr15_20729747-21193490.vcf.gz].sort.vcf.gz --INPUT [chr15_17000001-19725254.vcf.gz].sort.vcf.gz --INPUT [chr6_60001-58453888.vcf.gz].sort.vcf.gz --INPUT [chr10_47870369-124121200.vcf.gz].sort.vcf.gz --INPUT [chr22_11681289-11724629.vcf.gz].sort.vcf.gz --INPUT [chr9_41229379-41237752.vcf.gz].sort.vcf.gz --INPUT [chr20_29271827-29315342.vcf.gz].sort.vcf.gz --INPUT [chr11_88002897-135076622.vcf.gz].sort.vcf.gz --INPUT [chr7_61967064-61976104.vcf.gz].sort.vcf.gz --INPUT [chr16_33264596-33392411.vcf.gz].sort.vcf.gz --INPUT [chr3_10001-90565295.vcf.gz].sort.vcf.gz --INPUT [chr18_15791048-20564714.vcf.gz].sort.vcf.gz --INPUT [chrX_37285838-49348394.vcf.gz].sort.vcf.gz --INPUT [chr3_91256422-91257890.vcf.gz].sort.vcf.gz --INPUT [chr5_139453660-155760324.vcf.gz].sort.vcf.gz --INPUT [chr17_26698999-26720420.vcf.gz].sort.vcf.gz --INPUT [chr19_60001-24448980.vcf.gz].sort.vcf.gz --INPUT [chr22_12488691-12641730.vcf.gz].sort.vcf.gz --INPUT [chr13_86252980-111703855.vcf.gz].sort.vcf.gz --INPUT [chr1_143184588-223558935.vcf.gz].sort.vcf.gz --INPUT [chr21_10269869-10274327.vcf.gz].sort.vcf.gz --INPUT [chr1_122026460-124977944.vcf.gz].sort.vcf.gz --INPUT [chr6_61371373-95020790.vcf.gz].sort.vcf.gz --INPUT [chr15_84320067-101981189.vcf.gz].sort.vcf.gz --INPUT [chr8_60001-7617127.vcf.gz].sort.vcf.gz --INPUT [chrX_58605580-62412542.vcf.gz].sort.vcf.gz --INPUT [chr10_42066266-47780368.vcf.gz].sort.vcf.gz --INPUT [chr20_26436233-26590875.vcf.gz].sort.vcf.gz --INPUT [chr5_10001-17530548.vcf.gz].sort.vcf.gz --OUTPUT joint_germline.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
  09:21:54.362 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/envs/python27/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  [Fri Feb 10 09:21:54 UTC 2023] MergeVcfs --INPUT [chr4_31832570-32833016.vcf.gz].sort.vcf.gz --INPUT [chr21_9246088-9377143.vcf.gz].sort.vcf.gz --INPUT [chr9_63968448-64135013.vcf.gz].sort.vcf.gz --INPUT [chr18_10001-15410899.vcf.gz].sort.vcf.gz --INPUT [chr21_5443559-5449012.vcf.gz].sort.vcf.gz --INPUT [chr6_95070791-167591393.vcf.gz].sort.vcf.gz --INPUT [chr22_10834644-10874572.vcf.gz].sort.vcf.gz --INPUT [chr22_18339130-18433513.vcf.gz].sort.vcf.gz --INPUT [chr21_12965809-43212462.vcf.gz].sort.vcf.gz --INPUT [chr10_39230137-39409792.vcf.gz].sort.vcf.gz --INPUT [chr4_49486925-49658100.vcf.gz].sort.vcf.gz --INPUT [chr22_12275589-12438690.vcf.gz].sort.vcf.gz --INPUT [chr16_46380683-90228345.vcf.gz].sort.vcf.gz --INPUT [chr22_11118988-11160921.vcf.gz].sort.vcf.gz --INPUT [chr1_228608365-248946422.vcf.gz].sort.vcf.gz --INPUT [chrY_10682443-10691573.vcf.gz].sort.vcf.gz --INPUT [chr4_8816478-9272916.vcf.gz].sort.vcf.gz --INPUT [chr3_90568829-90722458.vcf.gz].sort.vcf.gz --INPUT [chr21_43262463-46699983.vcf.gz].sort.vcf.gz --INPUT [chr18_54537529-80263285.vcf.gz].sort.vcf.gz --INPUT [chr11_71055697-87978202.vcf.gz].sort.vcf.gz --INPUT [chr10_124121503-133690466.vcf.gz].sort.vcf.gz --INPUT [chr17_491112-21795850.vcf.gz].sort.vcf.gz --INPUT [chr13_111843442-113673020.vcf.gz].sort.vcf.gz --INPUT [chr12_10001-7083650.vcf.gz].sort.vcf.gz --INPUT [chr12_7084651-34719407.vcf.gz].sort.vcf.gz --INPUT [chr4_10001-1429358.vcf.gz].sort.vcf.gz --INPUT [chr21_8099840-8260971.vcf.gz].sort.vcf.gz --INPUT [chr9_134185537-138334717.vcf.gz].sort.vcf.gz --INPUT [chr9_63008372-63202862.vcf.gz].sort.vcf.gz --INPUT [chr8_7667128-12234345.vcf.gz].sort.vcf.gz --INPUT [chrY_56673215-56771509.vcf.gz].sort.vcf.gz --INPUT [chr21_10324328-10814560.vcf.gz].sort.vcf.gz --INPUT [chr2_91402512-92138145.vcf.gz].sort.vcf.gz --INPUT [chr11_51078349-54425074.vcf.gz].sort.vcf.gz --INPUT [chr10_38573339-38906036.vcf.gz].sort.vcf.gz --INPUT [chr1_125173584-125184587.vcf.gz].sort.vcf.gz --INPUT [chr8_85714223-145078636.vcf.gz].sort.vcf.gz --INPUT [chr6_167641394-170745979.vcf.gz].sort.vcf.gz --INPUT [chr9_10001-41225986.vcf.gz].sort.vcf.gz --INPUT [chr9_61785369-62149738.vcf.gz].sort.vcf.gz --INPUT [chr20_29413578-29562970.vcf.gz].sort.vcf.gz --INPUT [chr2_97489619-238903659.vcf.gz].sort.vcf.gz --INPUT [chr14_16133336-16140527.vcf.gz].sort.vcf.gz --INPUT [chr16_18486487-33214595.vcf.gz].sort.vcf.gz --INPUT [chr20_29697631-30038348.vcf.gz].sort.vcf.gz --INPUT [chrY_9055175-9057608.vcf.gz].sort.vcf.gz --INPUT [chr5_46485901-47069162.vcf.gz].sort.vcf.gz --INPUT [chr20_60001-63215.vcf.gz].sort.vcf.gz --INPUT [chr4_49708101-51743951.vcf.gz].sort.vcf.gz --INPUT [chr22_49975366-50808468.vcf.gz].sort.vcf.gz --INPUT [chr9_43236168-43263290.vcf.gz].sort.vcf.gz --INPUT [chr5_49666174-50059807.vcf.gz].sort.vcf.gz --INPUT [chrY_11013047-11016992.vcf.gz].sort.vcf.gz --INPUT [chr20_31161626-36314371.vcf.gz].sort.vcf.gz --INPUT [chr8_12284346-43983744.vcf.gz].sort.vcf.gz --INPUT [chr22_12691731-12726204.vcf.gz].sort.vcf.gz --INPUT [chr12_132224363-133265309.vcf.gz].sort.vcf.gz --INPUT [chr16_34339330-34521510.vcf.gz].sort.vcf.gz --INPUT [chr18_47019913-54536574.vcf.gz].sort.vcf.gz --INPUT [chr2_92188146-94090557.vcf.gz].sort.vcf.gz --INPUT [chr1_10001-207666.vcf.gz].sort.vcf.gz --INPUT [chr16_34580966-34584085.vcf.gz].sort.vcf.gz --INPUT [chr2_32917626-89330679.vcf.gz].sort.vcf.gz --INPUT [chr21_5010001-5166246.vcf.gz].sort.vcf.gz --INPUT [chr16_10001-18436486.vcf.gz].sort.vcf.gz --INPUT [chr11_60001-50821348.vcf.gz].sort.vcf.gz --INPUT [chrX_144475607-156030895.vcf.gz].sort.vcf.gz --INPUT [chr4_58921382-190123121.vcf.gz].sort.vcf.gz --INPUT [chr19_24891357-24898313.vcf.gz].sort.vcf.gz --INPUT [chr20_28868453-28890335.vcf.gz].sort.vcf.gz --INPUT [chr9_66591388-67920552.vcf.gz].sort.vcf.gz --INPUT [chr13_18171249-18358106.vcf.gz].sort.vcf.gz --INPUT [chr7_58169654-60828234.vcf.gz].sort.vcf.gz --INPUT [chr2_89753993-90402511.vcf.gz].sort.vcf.gz --INPUT [chr5_49609715-49611721.vcf.gz].sort.vcf.gz --INPUT [chr13_18408107-86202979.vcf.gz].sort.vcf.gz --INPUT [chr17_21814104-21984549.vcf.gz].sort.vcf.gz --INPUT [chr17_26935981-81742542.vcf.gz].sort.vcf.gz --INPUT [chr20_30456078-30761898.vcf.gz].sort.vcf.gz --INPUT [chr22_11428057-11497337.vcf.gz].sort.vcf.gz --INPUT [chr8_45927266-85664222.vcf.gz].sort.vcf.gz --INPUT [chr21_8310972-8472360.vcf.gz].sort.vcf.gz --INPUT [chr5_155761325-181478259.vcf.gz].sort.vcf.gz --INPUT [chr21_7377866-7500890.vcf.gz].sort.vcf.gz --INPUT [chr20_31051509-31107036.vcf.gz].sort.vcf.gz --INPUT [chr2_10001-16145119.vcf.gz].sort.vcf.gz --INPUT [chr2_16146120-32867130.vcf.gz].sort.vcf.gz --INPUT [chr22_16302844-16304296.vcf.gz].sort.vcf.gz --INPUT [chr1_29553836-121976459.vcf.gz].sort.vcf.gz --INPUT [chr5_50109808-139452659.vcf.gz].sort.vcf.gz --INPUT [chr16_34584623-36260386.vcf.gz].sort.vcf.gz --INPUT [chrY_11674124-20207793.vcf.gz].sort.vcf.gz --INPUT [chr12_34829238-37185252.vcf.gz].sort.vcf.gz --INPUT [chr4_190173122-190204555.vcf.gz].sort.vcf.gz --INPUT [chr1_13004385-16799163.vcf.gz].sort.vcf.gz --INPUT [chr5_17580549-46435900.vcf.gz].sort.vcf.gz --INPUT [chrX_114331199-115738949.vcf.gz].sort.vcf.gz --INPUT [chr1_16849164-29552233.vcf.gz].sort.vcf.gz --INPUT [chrY_56821510-56887902.vcf.gz].sort.vcf.gz --INPUT [chr20_28752591-28843401.vcf.gz].sort.vcf.gz --INPUT [chr7_143700805-159335973.vcf.gz].sort.vcf.gz --INPUT [chr20_30088349-30425128.vcf.gz].sort.vcf.gz --INPUT [chr17_22813680-26627010.vcf.gz].sort.vcf.gz --INPUT [chr15_20729747-21193490.vcf.gz].sort.vcf.gz --INPUT [chr15_17000001-19725254.vcf.gz].sort.vcf.gz --INPUT [chr6_60001-58453888.vcf.gz].sort.vcf.gz --INPUT [chr10_47870369-124121200.vcf.gz].sort.vcf.gz --INPUT [chr22_11681289-11724629.vcf.gz].sort.vcf.gz --INPUT [chr9_41229379-41237752.vcf.gz].sort.vcf.gz --INPUT [chr20_29271827-29315342.vcf.gz].sort.vcf.gz --INPUT [chr11_88002897-135076622.vcf.gz].sort.vcf.gz --INPUT [chr7_61967064-61976104.vcf.gz].sort.vcf.gz --INPUT [chr16_33264596-33392411.vcf.gz].sort.vcf.gz --INPUT [chr3_10001-90565295.vcf.gz].sort.vcf.gz --INPUT [chr18_15791048-20564714.vcf.gz].sort.vcf.gz --INPUT [chrX_37285838-49348394.vcf.gz].sort.vcf.gz --INPUT [chr3_91256422-91257890.vcf.gz].sort.vcf.gz --INPUT [chr5_139453660-155760324.vcf.gz].sort.vcf.gz --INPUT [chr17_26698999-26720420.vcf.gz].sort.vcf.gz --INPUT [chr19_60001-24448980.vcf.gz].sort.vcf.gz --INPUT [chr22_12488691-12641730.vcf.gz].sort.vcf.gz --INPUT [chr13_86252980-111703855.vcf.gz].sort.vcf.gz --INPUT [chr1_143184588-223558935.vcf.gz].sort.vcf.gz --INPUT [chr21_10269869-10274327.vcf.gz].sort.vcf.gz --INPUT [chr1_122026460-124977944.vcf.gz].sort.vcf.gz --INPUT [chr6_61371373-95020790.vcf.gz].sort.vcf.gz --INPUT [chr15_84320067-101981189.vcf.gz].sort.vcf.gz --INPUT [chr8_60001-7617127.vcf.gz].sort.vcf.gz --INPUT [chrX_58605580-62412542.vcf.gz].sort.vcf.gz --INPUT [chr10_42066266-47780368.vcf.gz].sort.vcf.gz --INPUT [chr20_26436233-26590875.vcf.gz].sort.vcf.gz --INPUT [chr5_10001-17530548.vcf.gz].sort.vcf.gz --OUTPUT joint_germline.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR . --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX true --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
  [Fri Feb 10 09:22:04 UTC 2023] Executing as root@26047e876e98 on Linux 3.10.0-862.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 11.0.13+7-b1751.21; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.3.0.0
  [Fri Feb 10 09:22:04 UTC 2023] picard.vcf.MergeVcfs done. Elapsed time: 0.18 minutes.
  Runtime.totalMemory()=2147483648
  To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
  htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to parse header with error: Not in GZIP format, for input source: file://%5Bchr4_31832570-32833016.vcf.gz%5D.sort.vcf.gz
  	at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:264)
  	at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:103)
  	at htsjdk.tribble.TribbleIndexedFeatureReader.<init>(TribbleIndexedFeatureReader.java:128)
  	at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:121)
  	at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:81)
  	at htsjdk.variant.vcf.VCFFileReader.<init>(VCFFileReader.java:145)
  	at picard.vcf.MergeVcfs.doWork(MergeVcfs.java:182)
  	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:309)
  	at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
  	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
  	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
  	at org.broadinstitute.hellbender.Main.main(Main.java:289)
  Caused by: java.util.zip.ZipException: Not in GZIP format
  	at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:166)
  	at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:80)
  	at java.base/java.util.zip.GZIPInputStream.<init>(GZIPInputStream.java:92)
  	at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:258)
  	... 11 more

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@FriederikeHanssen
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Could you attach the compelte .nextflow.log file?

@nagihayate
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command.log

@nagihayate
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it's this one?

@FriederikeHanssen
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FriederikeHanssen commented Feb 11, 2023 •
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no it should be in the directory you executed the workflow from. It is a hidden file

@FriederikeHanssen
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ah sorry, it is, it is just usually not called command.log.

@nagihayate
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nextflow.log

@nagihayate
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Is this one?

@nagihayate
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next_flow.log
or this one?

@FriederikeHanssen
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NOt exactly sure still, but I think this is related to meta map issues.

@YuxinShi0423
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Hi we were having the same issue running this pipeline on DNAnexus platform:
The BCFTOOLS_SORT process generates output file named as [HCC1395N.chr17_38877931-38878296.vcf.gz].sort.vcf.gz and causing failure in later MERGE_FREEBAYES because it is a invalid file path.

The root cause for it should be the incorrect path specification in the config both here:

sarek/conf/modules/freebayes.config

Line 38 in c87f4eb

ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" }

and here:

sarek/conf/modules/haplotypecaller.config

Line 69 in c87f4eb

ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.joint.sort" : "${vcf.minus("vcf.gz")}.sort" }

This specification was updated in this commit 4e30625#diff-bf809c928cb10b54d251dec8a140a2d5505150f97175d8d7b51dda9cc57971feR567
But the "${vcf.minus("vcf.gz")} is not a correct/standard method to subtract substring from a path in nextflow.

We had fixed it manually and it worked on our platform. Please help check if it is indeed the cause and let me know if you have any suggestions. Thanks!

@commandlinegirl
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Would you be able to look at this @maxulysse, @FriederikeHanssen, or @drpatelh? It seems the path corrections @YuxinShi0423 mentions above as a fix should be rather straight-forward. Thank you so much for checking this!

@robsyme
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robsyme commented Jun 14, 2023

I support Yuxin Shi's diagnosis. To remove the .vcf.gz suffix, we need to call the minus method on a String, but at the moment, we're calling minus on the vcf object, which is some class that implements the java.nio.file.Path interface (the exact class depends on where you're running the workflow).

Let's take a simple example:

process MakeFiles {
    output: path("*")
    script: "touch example.vcf.gz"
}

workflow {
    MakeFiles | view { it.getClass() }
}

Shows (on my machine):

❯ nextflow run .
N E X T F L O W  ~  version 23.04.1
Launching `./main.nf` [cheeky_elion] DSL2 - revision: d59bed4add
executor >  local (1)
[38/f9ff50] process > MakeFiles [100%] 1 of 1 ✔
class sun.nio.fs.UnixPath

This UnixPath class implements the java.nio.fs.Path interface, so all of these methods are available. Note there, the minus method is defined on the Path class, but that minus method is the one inherited from java.lang.Iterable because Paths are also iterable.
This minus method is used to remove an element from an iterable object (so, removing a Path from a Path). For example, I could use the minus method (aliased to -) to subtract paths:

workflow {
    MakeFiles | view { it - workflow.projectDir }
}

With that aside done, what we actually want to do in this case is use the minus method defined on a String to remove the suffix. In this case, we need to use the .getName() method (aliased to .name) which will return a string.:

ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.name.minus("vcf")}.sort" } 
// or something like:
ext.prefix = { meta.num_intervals <= 1 ? meta.id + "freebayes" : vcf.name - ".vcf" + ".sort" }

@maxulysse maxulysse mentioned this issue Jun 14, 2023
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@maxulysse
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PR has been merge.
So it's fixed in dev, and we're planning a release soon

@YuxinShi0423
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Thanks @maxulysse @robsyme and @commandlinegirl ! Glad to help :)

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@robsyme @maxulysse @commandlinegirl @FriederikeHanssen @YuxinShi0423 @nagihayate