Running your Demo

[Brent-Saylor-Canopy]

Hi,

I would love to give your pipeline a try, however I have to admit I am having trouble figuring out the inputs for the demo. I tried the following command

perl ../bsa.pipeline.pl \
  -vcf pop.BSA.vcf \
  -pid R01,R02, \
  -bid R03,R04 \
  -bs 38 \
  -out Test_out 

I'm guessing on the parent and bulk names from the vcf file, but I don't what to put in the annotation field. Is it also required? also I have a VCF file with one parent and the two bulks. Is it possible to use this data with your pipeline?

Thanks in advance for your help

[czheluo]

Hi, @Brent-Saylor-Canopy

Could you provide your vcf file for me (no all data need), and the annotation file no need for sure. You can post your error here, let me check.

[Brent-Saylor-Canopy]

HI, For now I'm just trying to run the demo file from found on your repro to run so I can understand how to generate the proper inputs. I am working with a non-reference genome, and data I can't share so the demo seemed the best first step. The demo file I'm using can be found at https://github.com/czheluo/MBSA/tree/master/demo

[Brent-Saylor-Canopy]

The error I'm getting is the following. I'm running on a stock ubuntu distro.
Is slurm required to run the script?

"my" variable $out masks earlier declaration in same scope at /opt/MBSA/bin/step01.vcf-convert.pl line 26.
Can't exec "qsub-slurm.pl": No such file or directory at /opt/MBSA/bin/step01.vcf-convert.pl line 54.
Can't exec "qsub-slurm.pl": No such file or directory at /opt/MBSA/bin/step02.bsaRData.pl line 57.
Use of uninitialized value $ann in concatenation (.) or string at ../bsa.pipeline.pl line 72.
"my" variable $int masks earlier declaration in same scope at /opt/MBSA/bin/step03.bsaED.pl line 26.
Can't exec "qsub-slurm.pl": No such file or directory at /opt/MBSA/bin/step03.bsaED.pl line 55.
Use of uninitialized value $ann in concatenation (.) or string at ../bsa.pipeline.pl line 85.
Can't exec "qsub-slurm.pl": No such file or directory at /opt/MBSA/bin/step04.bsaIndex.pl line 70.
Use of uninitialized value $ann in concatenation (.) or string at ../bsa.pipeline.pl line 98.
Can't exec "qsub-slurm.pl": No such file or directory at /opt/MBSA/bin/step05.bsaGprime.pl line 63.
Use of uninitialized value $ann in concatenation (.) or string at ../bsa.pipeline.pl line 111.
Can't exec "qsub-slurm.pl": No such file or directory at /opt/MBSA/bin/step06.bsaBSR.pl line 44.

Done. Total elapsed time : 0s`
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