[Sciapps-support] Issues with running BSA-seq workflow

[Frank Harmon]

Dear SciApps,
My student and I are both having trouble running the BSA-seq pipeline on SciApps. Each of us is rerunning the demonstration analysis for mapping the ms9 mutant. I did this successfully in November 2020. Ultimately, we want to map a new mutant with our own sequencing data, but want to confirm the workflow first.
Now, the Bowtie2 job fails soon after relaunching the BSA-seq workflow and selecting Submit. I have tried copying the ms9_x.fq.gz sequence files to my sci_data folder, but this did not help. I also started Bowtie2 alone and it failed in a similar way. Attempts to run STAR_align and BWA_mem also fail.
I also receive the warning “A sci_data” folder is needed…” when I submit the job. Is this normal?
My Cyverse username is fharmon.
I appreciate any suggestions to correct this issue. Thank you.
Sincerely,
Frank



——
Frank G. Harmon, PhD
Principal Investigator
Plant Gene Expression Center
Albany, CA




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