<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear SciApps,<div class="">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.</div><div class="">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.</div><div class="">I also receive the warning “A sci_data” folder is needed…” when I submit the job. Is this normal?</div><div class="">My Cyverse username is fharmon.</div><div class="">I appreciate any suggestions to correct this issue. Thank you.</div><div class="">Sincerely,</div><div class="">Frank</div><div class=""><br class=""></div><br class=""><br class=""><div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;">——<br class="">Frank G. Harmon, PhD<br class="">Principal Investigator<br class="">Plant Gene Expression Center<br class="">Albany, CA</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></div><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline">
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