When running downstream script bam_stat_run_parallel.pbs, the following error occurred and was noted in the /Logs
../QC_reports/test_final_bams/S1.final.bam does NOT exists
This was due to the the variable $bam= in the bam_stat_make_input.sh, which is defined as
#bam=${outdir}/${sampleid}.final.bam and is thus creating an the entry in the /Inputs/bam_stat.inputs file below:
<sample>,../QC_reports/<cohort>_final_bams/<sample>.final.bam,
resulting in the error
../QC_reports/<cohort>_final_bams/<sampl>.final.bam does NOT exists
bam_stat.sh expects the input below:
<sample>,../<cohor>_final_bams/<sample>.final.bam,
Which was corrected by supplying the bamdir=../${cohort}_final_bams directory and
changing the bam= variable in bam_stat_make_input.sh to
bam=${bamdir}/${sampleid}.final.bam
When running downstream script
bam_stat_run_parallel.pbs, the following error occurred and was noted in the /Logs../QC_reports/test_final_bams/S1.final.bam does NOT existsThis was due to the the variable
$bam=in thebam_stat_make_input.sh, which is defined as#bam=${outdir}/${sampleid}.final.bamand is thus creating an the entry in the /Inputs/bam_stat.inputs file below:<sample>,../QC_reports/<cohort>_final_bams/<sample>.final.bam,resulting in the error../QC_reports/<cohort>_final_bams/<sampl>.final.bam does NOT existsbam_stat.sh expects the input below:
<sample>,../<cohor>_final_bams/<sample>.final.bam,Which was corrected by supplying the
bamdir=../${cohort}_final_bamsdirectory and changing thebam=variable in bam_stat_make_input.sh tobam=${bamdir}/${sampleid}.final.bam