Error when removing contamination

[carolynzy]

Hi,

I'm trying to remove contamination using the following commands:

$nextflow run ~/clockwork/nextflow/remove_contam.nf -with-singularity ~/clockwork/singularity/clockwork_container.img --ref_fasta ~/clockwork/ref_data/OUT/ref.fa --ref_metadata_tsv ~/clockwork/ref_data/OUT/remove_contam_metadata.tsv --reads_in1 1_1.fq --reads_in2 1_2.fq --outprefix remove_contam.out

and got the error message:

N E X T F L O W ~ version 20.10.0
Launching /home/carolyn/clockwork/nextflow/remove_contam.nf [lonely_church] - revision: b2f84f8ad4
executor > local (1)
[9d/405c46] process > make_jobs_tsv [ 0%] 0 of 1
[- ] process > map_reads -
[- ] process > sam_to_fastq_files -
executor > local (1)
[9d/405c46] process > make_jobs_tsv [100%] 1 of 1, failed: 1 ✘
[- ] process > map_reads -
[- ] process > sam_to_fastq_files -
Error executing process > 'make_jobs_tsv'

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

Command executed:

echo "reads_in1 reads_in2 counts_tsv reads_contam1 reads_contam2 reads_remove_contam1 reads_remove_contam2 sample_id seqrep_id isolate_id sequence_replicate_number reference_id ref_fasta contam_tsv" > tmp.tsv
echo "/media/carolyn/8T/fastq_rmcontam_clockwork/1_1.fq /media/carolyn/8T/fastq_rmcontam_clockwork/1_2.fq /media/carolyn/8T/fastq_rmcontam_clockwork/remove_contam.out.counts.tsv /media/carolyn/8T/fastq_rmcontam_clockwork/remove_contam.out.contam.1.fq.gz /media/carolyn/8T/fastq_rmcontam_clockwork/remove_contam.out.contam.2.fq.gz /media/carolyn/8T/fastq_rmcontam_clockwork/remove_contam.out.remove_contam.1.fq.gz /media/carolyn/8T/fastq_rmcontam_clockwork/remove_contam.out.remove_contam.2.fq.gz . . . . . /home/carolyn/clockwork/ref_data/OUT/ref.fa /home/carolyn/clockwork/ref_data/OUT/remove_contam_metadata.tsv" >> tmp.tsv
sed 's/ / /g' tmp.tsv > jobs_tsv
rm tmp.tsv

Command exit status:
1

Command output:
(empty)

Command error:
/bin/bash: line 0: cd: /media/carolyn/8T/fastq_rmcontam_clockwork/work/9d/405c46ed86f696e8fc74ab97c6cde7: No such file or directory
/bin/bash: .command.sh: No such file or directory

Work dir:
/media/carolyn/8T/fastq_rmcontam_clockwork/work/9d/405c46ed86f696e8fc74ab97c6cde7

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

The messages says "/media/carolyn/8T/fastq_rmcontam_clockwork/work/9d/405c46ed86f696e8fc74ab97c6cde7: No such file or directory' , but the directory is there. I'm not sure whether this is the problem or something else went wrong. Any idea?