The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'analyze_af_report (1)'
Caused by:
Process `analyze_af_report (1)` terminated with an error exit status (1)
Command executed:
cp analyze_af_report.Rmd MAD_report.Rmd
R -e "af_report = 'spontaneous_ptolemy_af_data.csv'; golden_vcf = 'modes_test_AF_0.05.vcf'; rmarkdown::render('MAD_report.Rmd')"
Command exit status:
1
Command output:
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label: unnamed-chunk-2
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ordinary text without R code
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label: unnamed-chunk-3
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ordinary text without R code
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label: unnamed-chunk-4
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ordinary text without R code
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label: unnamed-chunk-5
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ordinary text without R code
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label: unnamed-chunk-6
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ordinary text without R code
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label: unnamed-chunk-7
Command error:
processing file: MAD_report.Rmd
Quitting from lines 156-184 (MAD_report.Rmd)
Error in `$<-.data.frame`(`*tmp*`, category, value = "FP") :
replacement has 1 row, data has 0
Calls: ... withVisible -> eval -> eval -> $<- -> $<-.data.frame
Execution halted
Work dir:
/scratch/mk5636/nextflow_work_dir/13/ec9931bd6057a9428a3e1544c98bfc
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
nextflow run main.nf -c test.config -with-singularity 'gencorefacility/mad:1' -with-report test-report.htmlad67cae990647683338f15b7aafb5e7a8c3c8638-9ffd-4232-9f79-8952d887fc1fThese plots give an overview of the distribution of resource usage for each process.
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