trimReads fails: no file sample1_artic_R_covid_1_val_1.fq.gz

[stephlo76]

When I try the pipeline with the example samples provided, it crashes during the trimReads step. TrimGalore runs fine, but after that, a file named sample1_artic_R_covid_1_val_1.fq.gz is missing. I do not see where that file should come from. I had to run it without kraken2db since that file was not provided any more.

Command:
nextflow run czbiohub/sc2-illumina-pipeline -profile artic,conda --reads 'sc2-illumina-pipeline/test_data/sample1_artic_R{1,2}.fq.gz' --outdir 'test_sc2' --max_memory '8GB' --max_cpus 8

Complete output: N E X T F L O W ~ version 21.04.0
Launching czbiohub/sc2-illumina-pipeline [focused_poincare] - revision: d7f3a8a0ef [master]
executor > local (5)
[- ] process > prefilterHostReads -
[77/765eeb] process > quantifyERCCs (sample1_artic_R) [100%] 1 of 1 ✔
[- ] process > filterReads -
[d6/d3d0da] process > trimReads (sample1_artic_R) [ 75%] 3 of 4, failed: 3, retries: 3
[- ] process > alignReads -
[- ] process > trimPrimers -
[- ] process > samtoolsDepth -
[- ] process > makeConsensus -
[- ] process > quast -
[- ] process > callVariants -
[- ] process > filterVariants -
[- ] process > computeStats -
[- ] process > mergeVcfs -
[- ] process > combinedVariants -
[- ] process > mergeAllAssemblies -
[- ] process > mergeAssemblyStats -
[- ] process > filterAssemblies -
[- ] process > snpsDf -
[- ] process > qcTreeMap -
[- ] process > multiqc -
[a2/0dc596] NOTE: Process trimReads (sample1_artic_R) terminated with an error exit status (1) -- Execution is retried (1)
[72/c0e032] NOTE: Process trimReads (sample1_artic_R) terminated with an error exit status (1) -- Execution is retried (2)
[34/4c6677] NOTE: Process trimReads (sample1_artic_R) terminated with an error exit status (1) -- Execution is retried (3)
Error executing process > 'trimReads (sample1_artic_R)'

Caused by:
Process trimReads (sample1_artic_R) terminated with an error exit status (1)

Command executed:

LINES=$(zcat sample1_artic_R1.fq.gz | wc -l)
if [ "$LINES" -gt 0 ];
then
trim_galore --fastqc --paired sample1_artic_R1.fq.gz sample1_artic_R2.fq.gz
TRIMMED=$(zcat sample1_artic_R_covid_1_val_1.fq.gz | wc -l)
if [ "$TRIMMED" == 0 ];
then
rm -r *fastqc.zip
fi
else
cp sample1_artic_R1.fq.gz sample1_artic_R_covid_1_val_1.fq.gz
cp sample1_artic_R2.fq.gz sample1_artic_R_covid_2_val_2.fq.gz
fi

Command exit status:
1

Command output:
Analysis complete for sample1_artic_R1_val_1.fq.gz
Analysis complete for sample1_artic_R2_val_2.fq.gz

Command error:

Now running FastQC on the validated data sample1_artic_R1_val_1.fq.gz<<<

Started analysis of sample1_artic_R1_val_1.fq.gz
Approx 5% complete for sample1_artic_R1_val_1.fq.gz
Approx 10% complete for sample1_artic_R1_val_1.fq.gz
Approx 15% complete for sample1_artic_R1_val_1.fq.gz
Approx 20% complete for sample1_artic_R1_val_1.fq.gz
Approx 25% complete for sample1_artic_R1_val_1.fq.gz
Approx 30% complete for sample1_artic_R1_val_1.fq.gz
Approx 35% complete for sample1_artic_R1_val_1.fq.gz
Approx 40% complete for sample1_artic_R1_val_1.fq.gz
Approx 45% complete for sample1_artic_R1_val_1.fq.gz
Approx 50% complete for sample1_artic_R1_val_1.fq.gz
Approx 55% complete for sample1_artic_R1_val_1.fq.gz
Approx 60% complete for sample1_artic_R1_val_1.fq.gz
Approx 65% complete for sample1_artic_R1_val_1.fq.gz
Approx 70% complete for sample1_artic_R1_val_1.fq.gz
Approx 75% complete for sample1_artic_R1_val_1.fq.gz
Approx 80% complete for sample1_artic_R1_val_1.fq.gz
Approx 85% complete for sample1_artic_R1_val_1.fq.gz
Approx 90% complete for sample1_artic_R1_val_1.fq.gz
Approx 95% complete for sample1_artic_R1_val_1.fq.gz

executor > local (5)
[- ] process > prefilterHostReads -
[77/765eeb] process > quantifyERCCs (sample1_artic_R) [100%] 1 of 1 ✔
[- ] process > filterReads -
[d6/d3d0da] process > trimReads (sample1_artic_R) [100%] 4 of 4, failed: 4, retries: 3 ✘
[- ] process > alignReads -
[- ] process > trimPrimers -
[- ] process > samtoolsDepth -
[- ] process > makeConsensus -
[- ] process > quast -
[- ] process > callVariants -
[- ] process > filterVariants -
[- ] process > computeStats -
[- ] process > mergeVcfs -
[- ] process > combinedVariants -
[- ] process > mergeAllAssemblies -
[- ] process > mergeAssemblyStats -
[- ] process > filterAssemblies -
[- ] process > snpsDf -
[- ] process > qcTreeMap -
[- ] process > multiqc -
Execution cancelled -- Finishing pending tasks before exit
[a2/0dc596] NOTE: Process trimReads (sample1_artic_R) terminated with an error exit status (1) -- Execution is retried (1)
[72/c0e032] NOTE: Process trimReads (sample1_artic_R) terminated with an error exit status (1) -- Execution is retried (2)
[34/4c6677] NOTE: Process trimReads (sample1_artic_R) terminated with an error exit status (1) -- Execution is retried (3)
Error executing process > 'trimReads (sample1_artic_R)'

Caused by:
Process trimReads (sample1_artic_R) terminated with an error exit status (1)

Command executed:

LINES=$(zcat sample1_artic_R1.fq.gz | wc -l)
if [ "$LINES" -gt 0 ];
then
trim_galore --fastqc --paired sample1_artic_R1.fq.gz sample1_artic_R2.fq.gz TRIMMED=$(zcat sample1_artic_R_covid_1_val_1.fq.gz | wc -l) if [ "$TRIMMED" == 0 ]; then rm -r *fastqc.zip fi else cp sample1_artic_R1.fq.gz sample1_artic_R_covid_1_val_1.fq.gz cp sample1_artic_R2.fq.gz sample1_artic_R_covid_2_val_2.fq.gz fi

Command exit status: 1

Command output: Analysis complete for sample1_artic_R1_val_1.fq.gz Analysis complete for sample1_artic_R2_val_2.fq.gz

Command error:

Now running FastQC on the validated data sample1_artic_R1_val_1.fq.gz<<<

Started analysis of sample1_artic_R1_val_1.fq.gz Approx 5% complete for sample1_artic_R1_val_1.fq.gz Approx 10% complete for sample1_artic_R1_val_1.fq.gz Approx 15% complete for sample1_artic_R1_val_1.fq.gz Approx 20% complete for sample1_artic_R1_val_1.fq.gz Approx 25% complete for sample1_artic_R1_val_1.fq.gz Approx 30% complete for sample1_artic_R1_val_1.fq.gz Approx 35% complete for sample1_artic_R1_val_1.fq.gz Approx 40% complete for sample1_artic_R1_val_1.fq.gz Approx 45% complete for sample1_artic_R1_val_1.fq.gz Approx 50% complete for sample1_artic_R1_val_1.fq.gz Approx 55% complete for sample1_artic_R1_val_1.fq.gz Approx 60% complete for sample1_artic_R1_val_1.fq.gz Approx 65% complete for sample1_artic_R1_val_1.fq.gz Approx 70% complete for sample1_artic_R1_val_1.fq.gz Approx 75% complete for sample1_artic_R1_val_1.fq.gz Approx 80% complete for sample1_artic_R1_val_1.fq.gz Approx 85% complete for sample1_artic_R1_val_1.fq.gz Approx 90% complete for sample1_artic_R1_val_1.fq.gz Approx 95% complete for sample1_artic_R1_val_1.fq.gz

>>> Now running FastQC on the validated data sample1_artic_R2_val_2.fq.gz<<<

Started analysis of sample1_artic_R2_val_2.fq.gz Approx 5% complete for sample1_artic_R2_val_2.fq.gz Approx 10% complete for sample1_artic_R2_val_2.fq.gz Approx 15% complete for sample1_artic_R2_val_2.fq.gz Approx 20% complete for sample1_artic_R2_val_2.fq.gz Approx 25% complete for sample1_artic_R2_val_2.fq.gz Approx 30% complete for sample1_artic_R2_val_2.fq.gz Approx 35% complete for sample1_artic_R2_val_2.fq.gz Approx 40% complete for sample1_artic_R2_val_2.fq.gz Approx 45% complete for sample1_artic_R2_val_2.fq.gz Approx 50% complete for sample1_artic_R2_val_2.fq.gz Approx 55% complete for sample1_artic_R2_val_2.fq.gz Approx 60% complete for sample1_artic_R2_val_2.fq.gz Approx 65% complete for sample1_artic_R2_val_2.fq.gz Approx 70% complete for sample1_artic_R2_val_2.fq.gz Approx 75% complete for sample1_artic_R2_val_2.fq.gz Approx 80% complete for sample1_artic_R2_val_2.fq.gz Approx 85% complete for sample1_artic_R2_val_2.fq.gz Approx 90% complete for sample1_artic_R2_val_2.fq.gz Approx 95% complete for sample1_artic_R2_val_2.fq.gz Deleting both intermediate output files sample1_artic_R1_trimmed.fq.gz and sample1_artic_R2_trimmed.fq.gz

====================================================================================================

gzip: sample1_artic_R_covid_1_val_1.fq.gz: No such file or directory

Work dir: /home/stephan/work/d6/d3d0dad0d58841c9322ad8e2a36196

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh