The exit status of the task that caused the workflow execution to fail was: 143
.
The full error message was:
Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (HCC1395T_vs_HCC1395N)' Caused by: Host EC2 (instance i-023097555fc5565d7) terminated. Command executed: gatk --java-options "-Xmx58982M -XX:-UsePerfData" \ Mutect2 \ --input HCC1395N.recal.cram --input HCC1395T.recal.cram \ --output HCC1395T_vs_HCC1395N.mutect2.chr1_11981-12351.vcf.gz \ --reference Homo_sapiens_assembly38.fasta \ --panel-of-normals 1000g_pon.hg38.vcf.gz \ --germline-resource af-only-gnomad.hg38.vcf.gz \ --intervals chr1_11981-12351.bed \ --tmp-dir . \ --f1r2-tar-gz HCC1395T_vs_HCC1395N.mutect2.chr1_11981-12351.f1r2.tar.gz --normal-sample HCC1395_HCC1395N cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED": gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//') END_VERSIONS Command exit status: 143 Command output: (empty) Command error: (more omitted..) 15:32:04.653 INFO ProgressMeter - chr12:103930423 95.6 404990 4237.1 15:32:14.754 INFO ProgressMeter - chr12:107620159 95.8 405950 4239.7 15:32:24.761 INFO ProgressMeter - chr12:109535744 95.9 406890 4242.1 15:32:34.847 INFO ProgressMeter - chr12:111450116 96.1 407740 4243.5 15:32:45.002 INFO ProgressMeter - chr12:113187079 96.3 408710 4246.1 15:32:55.017 INFO ProgressMeter - chr12:118139742 96.4 409660 4248.6 15:33:05.184 INFO ProgressMeter - chr12:120764147 96.6 410550 4250.4 15:33:15.202 INFO ProgressMeter - chr12:122319419 96.8 411380 4251.7 15:33:25.259 INFO ProgressMeter - chr12:123618012 96.9 412250 4253.3 15:33:35.420 INFO ProgressMeter - chr12:125660116 97.1 413070 4254.3 15:33:45.585 INFO ProgressMeter - chr12:132150764 97.3 413880 4255.2 15:33:56.053 INFO ProgressMeter - chr13:18219632 97.4 414610 4255.1 15:34:06.092 INFO ProgressMeter - chr13:23590300 97.6 415510 4257.0 15:34:16.120 INFO ProgressMeter - chr13:26024494 97.8 416270 4257.5 15:34:26.200 INFO ProgressMeter - chr13:30621625 97.9 417040 4258.1 15:34:36.223 INFO ProgressMeter - chr13:34942847 98.1 417770 4258.3 15:34:46.275 INFO ProgressMeter - chr13:38692084 98.3 418420 4257.6 15:34:56.320 INFO ProgressMeter - chr13:41590440 98.4 418950 4255.8 15:35:06.322 INFO ProgressMeter - chr13:45401259 98.6 419530 4254.5 15:35:16.386 INFO ProgressMeter - chr13:48709392 98.8 420200 4254.0 15:35:26.394 INFO ProgressMeter - chr13:54041373 98.9 421270 4257.7 15:35:36.475 INFO ProgressMeter - chr13:77895440 99.1 422410 4261.9 15:35:46.589 INFO ProgressMeter - chr13:98021822 99.3 423360 4264.3 15:35:56.610 INFO ProgressMeter - chr13:102840345 99.4 424390 4267.5 15:36:06.672 INFO ProgressMeter - chr13:112485754 99.6 425270 4269.1 15:36:16.716 INFO ProgressMeter - chr14:19302024 99.8 426210 4271.4 15:36:26.781 INFO ProgressMeter - chr14:20369812 100.0 426490 4267.0 15:36:36.985 INFO ProgressMeter - chr14:21263716 100.1 427000 4264.9 15:36:47.060 INFO ProgressMeter - chr14:22499557 100.3 427590 4263.6 15:36:57.061 INFO ProgressMeter - chr14:23118762 100.5 428160 4262.2 15:37:07.189 INFO ProgressMeter - chr14:23567416 100.6 428650 4259.9 15:37:17.407 INFO ProgressMeter - chr14:24240405 100.8 429160 4257.8 15:37:27.682 INFO ProgressMeter - chr14:29577231 101.0 429680 4255.7 15:37:37.809 INFO ProgressMeter - chr14:33930882 101.1 430410 4255.8 15:37:47.888 INFO ProgressMeter - chr14:38212885 101.3 431220 4256.8 15:37:57.988 INFO ProgressMeter - chr14:49829433 101.5 432120 4258.6 15:38:08.018 INFO ProgressMeter - chr14:51860737 101.6 432830 4258.5 15:38:18.058 INFO ProgressMeter - chr14:54702542 101.8 433460 4257.7 15:38:28.124 INFO ProgressMeter - chr14:56898069 102.0 434020 4256.2 15:38:38.155 INFO ProgressMeter - chr14:60115902 102.1 434810 4257.0 15:38:48.167 INFO ProgressMeter - chr14:64030890 102.3 435580 4257.6 15:38:58.205 INFO ProgressMeter - chr14:67224739 102.5 436420 4258.8 15:39:08.533 INFO ProgressMeter - chr14:69090847 102.6 437040 4257.7 15:39:18.587 INFO ProgressMeter - chr14:72550813 102.8 437840 4258.6 15:39:28.603 INFO ProgressMeter - chr14:74065393 103.0 438610 4259.1 15:39:38.759 INFO ProgressMeter - chr14:75473021 103.2 439350 4259.3 15:39:48.823 INFO ProgressMeter - chr14:77181861 103.3 439860 4257.3 15:39:59.107 INFO ProgressMeter - chr14:79863435 103.5 440430 4255.8 15:40:09.237 INFO ProgressMeter - chr14:88185466 103.7 440870 4253.1 15:40:19.237 INFO ProgressMeter - chr14:89963196 103.8 441330 4250.7 Work dir: s3://nf-core-awsmegatests/work/sarek/work-5fe5cdff171e3baed603b3990cab7f7fd3fcb992/test_full/f9/4a5927f02be1df1e6e4f0a7ecb9597 Container: wave.seqera.io/wt/00c3bd280df9/biocontainers/gatk4:4.5.0.0--py36hdfd78af_0 Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
nextflow run 'https://github.com/nf-core/sarek' -name maniac_banach -params-file 'https://api.cloud.seqera.io/ephemeral/rtvmn3zSLm11V2eW-NdIcg.json' -with-tower -r 3.5.1 -profile test_full
3954909713023f4328e976337e6e2cb9
20a3eacb-9173-482b-a30d-fd49d9fceb79
https://github.com/nf-core/sarek
, revision 3.5.1
(commit hash 5fe5cdff171e3baed603b3990cab7f7fd3fcb992
)These plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.