sk-sahu
commented
3 years ago As @cgpu suggested
The error seems to be coming from this check:
if (args.task != 'prep' and args.stat
and (len(args.b1) * len(args.b2) == 0)
and (len(args.s1) * len(args.s2) == 0)):
sys.exit('ERROR: while performing statistical analysis, user should provide two groups of samples. Please check b1,b2 or s1,s2.')
We need to inspect if one of this conditions is violated but also find the actual version (this one is from the latest for quickness).
cgpu
angarb
As reported in this slack thread - Out of complete random sometime (because other times it work as expected) rmats process fails with this following error.
Faild jobs -
Success jobs -
The problem seems to be with defining b1 and b2. It looks like b1 is made correctly but for some reason b2 is blank.
This is something to do with the logic mentioned here to produce two files
b1.txtandb2.txt.I checked the error from back-end (work dir), although both files generated
b2.txtis empty.Reproducing try
To reproduce this I extrapolated this script from main.nf
test_group.nf (click to expand)
```nextflow bams = "old_job/MYC_high_vs_low_bams_forCloudOS_updated2.csv" rmats_pairs = "old_job/BRCA_MYC_low_v_high_rmatsPairs_revised3.txt" Channel .fromPath(bams) .ifEmpty { exit 1, "Cannot find BAMs csv file : ${bams}" } .splitCsv(skip:1) .map { name, bam, bai -> [ name, file(bam), file(bai) ] } .into { indexed_bam; indexed_bam_rmats } indexed_bam_rmats .map { name, bam, bai -> [name, bam] } .set { bam } Channel .fromPath(rmats_pairs) .ifEmpty { exit 1, "Cannot find rMATS pairs file : ${rmats_pairs}" } .splitCsv(sep:' ') .map { row -> def rmats_id = row[0] def b1 = row[1].toString().split(',') def b2 = row[2].toString().split(',') [ rmats_id, b1, b2 ] } .set { samples} samples .map { row -> def samples_rmats_id = [] def rmats_id = row[0] def b1_samples = row[1] def b2_samples = row[2] b1_samples.each { sample -> samples_rmats_id.add([sample, 'b1', rmats_id]) } b2_samples.each { sample -> samples_rmats_id.add([sample, 'b2', rmats_id]) } samples_rmats_id } .flatMap() .combine(bam, by:0) .map { sample_id, b, rmats_id, bam -> [ rmats_id + b, rmats_id, bam] } .groupTuple() .map { b, rmats_id, bams -> [rmats_id[0], [b, bams]] } .groupTuple() .map { rmats_id, bams -> def b1_bams = bams[0][0].toString().endsWith('b1') ? bams[0] : bams[1] def b2_bams = bams[0][0].toString().endsWith('b2') ? bams[0] : bams[1] rmats_id_bams = b2_bams == null ? [ rmats_id, b1_bams[1], "no b2", true ] : [ rmats_id, b1_bams[1] , b2_bams[1], false ] rmats_id_bams } .set { bams } //bams.view() process rmats { echo true input: set val(rmats_id), file(bams), file(b2_bams), val(b1_only) from bams script: if (b1_only) { b1_bams = bams.join(",") b2_cmd = '' b2_flag = '' b2_config_cmd = '' } else { b1_bams = bams.join(",") b2_bams = b2_bams.join(",") b2_cmd = "echo b2.txt $b2_bams" b2_flag = "--b2 b2.txt" b2_config_cmd = "echo b2 b2.txt >> \$rmats_config" } """ echo b1.txt $b1_bams $b2_cmd """ } ```
Run
but it works completely fine as expected (creates two
b1.txtandb2.txt).