Process `call_stars ()` terminated with an error exit status (1)

[TonyLupara]

Describe the bug When run on my data, the last process 'call stars' is terminated and no output alleles is generated. It produce only variants:

BWA-hs37d5.WGS_cyp2d6.vcf.gz BWA-hs37d5.WGS_cyp2d6.vcf.gz.tbi

Sorry, I didn't find the logs in work directory.

To Reproduce -Ubuntu 20.04 virtual machine on server -Singularity/Docker (same error) -N E X T F L O W ~ version 21.10.1 (same on DSL1 an DSL2) -command: nextflow run main.nf -profile standard --build hg19 --gene cyp2d6

Screenshots

[twesigomwedavid]

@TonyLupara,

Thanks. Kindly send a screenshot of the error in $PWD/work/c9/2e765a<tab_key>/.command.err

Also, could you confirm that you're using high coverage (~30x) WGS data as input?

Thanks

[TonyLupara]

@twesigomwedavid, Thank you for quick response! I actually use WGS with 34x coverage.

Traceback (most recent call last): File "bin/stellarpgx.py", line 28, in cn = get_total_CN(cov_file)[0] File "/home/tony-lupara/StellarPGx/scripts/cyp2d6/b37/bin/sv_modules.py", line 25, in get_total_CN av_2d7_ex2_in8 = float(all_reg[10][3])/(float(all_reg[10][2]) - float(all_reg[10][1])) IndexError: list index out of range

[twesigomwedavid]

@TonyLupara

Thanks. How about the content of the depth file in work/08/1ff463<tab_key>/

Also, is this error happening for all your samples or just this one

[TonyLupara]

@twesigomwedavid,

chr22 42522300 42522800 61140 chr22 42522000 42526000 473627 chr22 42520000 42531500 1234331 chr12 48235320 48298814 4470025 chr22 42526000 42531500 512865 chr22 42538400 42540600 237348 chr22 42535500 42538100 313146 chr7 55086678 55279262 9578555 chr22 42536550 42539583 324698 chr22 42539583 42540600 118488

I find that it missing 2 regions from ~/resources/cyp2d6/cyp_hg19/test3.bed: chr22 42535490 42536560 chr22 42536550 42538400

I've tried it only on 1 sample, waiting to process another sample's bam.

[twesigomwedavid]

@TonyLupara,

Thanks. This was caused by a delimiter issue i.e. those 2 lines had spaces instead of a '\t' delimiter in the BED file.

Please download the fix to your local StellarPGx directory using:

git stash
git pull
git stash pop 

[TonyLupara]

Excellent, it works!

@twesigomwedavid, thank you so much for your help!