GitLab

Hi, An user, skim17, reported an error generated during the 'trim' step such as [Process trim (3) terminated with an error exit status (1)]. After looking at the relevant scripts, we suspect that the error came from some lines in 'trimgalore.sh' below:

r1base="${fq1%.fastq*}" r2base="${fq2%.fastq*}" source /etc/profile.d/modules.sh module load trimgalore/0.4.1 cutadapt/1.9.1

if [ -s $fq2 ] then trim_galore --paired -q 25 --illumina --gzip --length 35 ${fq1} ${fq2} mv ${r1base}_val_1.fq.gz ${pair_id}.trim.R1.fastq.gz mv ${r2base}_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz else trim_galore -q 25 --illumina --gzip --length 35 ${fq1} mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz fi

because the user's fastq file names are in a format of 'SampleID_ReplicateNumber_ReadNumber.fq.gz', e.g. 'ff_Cre_1_1.fq.gz'. In this case 'r1base' and 'r2base' are invalid.