yanboANU
commented
4 years ago Thanks for you advice, I will update my code soon.
Yanbo Li 4.32, Building 145 (Hanna Neumann) Research School of Computer Science The Australian National University
Email: yanbo.li@anu.edu.aumailto:yu.lin@anu.edu.au
From: Timothy Rhyker Ranallo-Benavidez notifications@github.com Sent: Thursday, August 6, 2020 7:39 AM To: yanboANU/Kmer2SNP Kmer2SNP@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [yanboANU/Kmer2SNP] Empty hete.peak.k$1 file created if Rscript line fails (#6)
Hello,
On line 24 of runkmercalling.sh, the code will create an empty hete.peak.k$1 file if Rscript is unable to properly run. This causes issues when trying to rerun Kmer2SNP after fixing the Rscript issue. Would it be possible to make Kmer2SNP not produce a file if there is an error. For example, perhaps changing the line to:
out=$(Rscript /path2Kmer2SNP/Kmer2SNP/libprism/local/runfindGSE.r chr_k$1.histo $1 ./ $2) && echo "$out" > hete.peak.k$1
according to https://stackoverflow.com/questions/31424456/how-to-redirect-output-of-a-program-only-if-it-succeeded. Thanks.
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Hello,
On line 24 of runkmercalling.sh, the code will create an empty hete.peak.k$1 file if Rscript is unable to properly run. This causes issues when trying to rerun Kmer2SNP after fixing the Rscript issue. Would it be possible to make Kmer2SNP not produce a file if there is an error. For example, perhaps changing the line to:
out=$(Rscript /path2Kmer2SNP/Kmer2SNP/libprism/local/runfindGSE.r chr_k$1.histo $1 ./ $2) && echo "$out" > hete.peak.k$1
according to https://stackoverflow.com/questions/31424456/how-to-redirect-output-of-a-program-only-if-it-succeeded. Thanks.