tom-dyar
commented
5 years ago Yes, that appears to be a problem. We will need to figure out a workaround…
From: "B. Arman Aksoy" notifications@github.com
Reply-To: NCBI-Hackathons/MASSIF-BLAST reply@reply.github.com
Date: Saturday, September 29, 2018 at 6:16 PM
To: NCBI-Hackathons/MASSIF-BLAST MASSIF-BLAST@noreply.github.com
Cc: Subscribed subscribed@noreply.github.com
Subject: [NCBI-Hackathons/MASSIF-BLAST] Confirm that use of BLAST's -max_target_seqs is intentional (#9)
Hi there,
This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:
Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflowshttps://urldefense.proofpoint.com/v2/url?u=https-3A__academic.oup.com_bioinformatics_advance-2Darticle-2Dabstract_doi_10.1093_bioinformatics_bty833_5106166-3FredirectedFrom-3Dfulltext&d=DwMCaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=Wpxr3yZIgJUDc4CsPhUpuiAtTKDn_lya4DWla3Q21iI&m=qpeq-WZ_UKnBCE1Qp32Cucbgc1le7Yj8Y3OUsaR4Mic&s=irchmOY29NkamP_bELzFObxDoKbIsvqtQ3wuNc3CmwE&e=, there is a strong chance that this parameter is misused in your repository.
If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.
Thank you! -- Arman (armish/blast-patrolhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_armish_blast-2Dpatrol&d=DwMCaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=Wpxr3yZIgJUDc4CsPhUpuiAtTKDn_lya4DWla3Q21iI&m=qpeq-WZ_UKnBCE1Qp32Cucbgc1le7Yj8Y3OUsaR4Mic&s=KRDaaUG-_0SHbIM-prreYzt3bSWg6o1XujdXJtyf37U&e=)
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_NCBI-2DHackathons_MASSIF-2DBLAST_issues_9&d=DwMCaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=Wpxr3yZIgJUDc4CsPhUpuiAtTKDn_lya4DWla3Q21iI&m=qpeq-WZ_UKnBCE1Qp32Cucbgc1le7Yj8Y3OUsaR4Mic&s=SmN3CJTVNLCBVnBB7RPHM3IJQR55ADXnBEvTxaPr0OI&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AIfLuWnIztvIIml1KzfKfNgHFzl7JLxSks5uf-5FEtgaJpZM4XAtSa&d=DwMCaQ&c=n7UHtw8cUfEZZQ61ciL2BA&r=Wpxr3yZIgJUDc4CsPhUpuiAtTKDn_lya4DWla3Q21iI&m=qpeq-WZ_UKnBCE1Qp32Cucbgc1le7Yj8Y3OUsaR4Mic&s=JuqQbQK0fc_nPh0dPU7cxZN4n5wkxJZcz-6o9T4iS-c&e=.
Hi there,
This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's
-max_target_seqsparameter:Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.
If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.
Thank you! -- Arman (armish/blast-patrol)