Nextflow workflow report

[maniac_banach]

Workflow execution completed unsuccessfully!

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`
Run times
24-Mar-2025 10:10:38 - 24-Mar-2025 15:40:55 (duration: 5h 30m 18s)
  192 succeeded  
  0 cached  
  0 ignored  
  9 failed  
Nextflow command
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
CPU-Hours
106.4 (31% failed)
Launch directory
/
Work directory
s3://nf-core-awsmegatests/work/sarek/work-5fe5cdff171e3baed603b3990cab7f7fd3fcb992/test_full
Project directory
/.nextflow/assets/nf-core/sarek
Script name
main.nf
Script ID
3954909713023f4328e976337e6e2cb9
Workflow session
20a3eacb-9173-482b-a30d-fd49d9fceb79
Workflow repository
https://github.com/nf-core/sarek, revision 3.5.1 (commit hash 5fe5cdff171e3baed603b3990cab7f7fd3fcb992)
Workflow profile
test_full
Wave enabled
true
Fusion enabled
true, version 2.4
Nextflow version
version 24.10.4, build 5934 (20-01-2025 16:47 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

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.

(tasks table omitted because the dataset is too big)