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plachetzki / EYS_PROM

Phylogenetic data for paper with A. Zelhof on the origins of open rhabdoms
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Confirm that use of BLAST's `-max_target_seqs` is intentional #1

Open armish opened 5 years ago

armish commented 5 years ago

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 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)

plachetzki commented 5 years ago

Hi Armon,

Thanks for pointing this out. We always obtain fewer hits than the max seqs parameter for a given e value, so it should not effect our analyses. That note did clarify things, however.

Best

Dave

Sent from my iPad

On Sep 29, 2018, at 8:30 PM, B. Arman Aksoy notifications@github.com<mailto:notifications@github.com> wrote:

Caution - External Email

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=c6MrceVCY5m5A_KAUkrdoA&r=gZl-jyQbfCQIs8dZ3FKCzwt0Dm_uEXeB_OX1lbaJOQs&m=UYm6HdKV6A2sDSM4As_fiej7L8YpmP51SazL0xKK6nk&s=xxjthR2H-bAScZs_XczOpCZDWYqU7AmmAetupunFCRo&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=c6MrceVCY5m5A_KAUkrdoA&r=gZl-jyQbfCQIs8dZ3FKCzwt0Dm_uEXeB_OX1lbaJOQs&m=UYm6HdKV6A2sDSM4As_fiej7L8YpmP51SazL0xKK6nk&s=2f2kcwv0gY7IIL33HD-OWDk5bPeVzU6ylZLm0upOoV0&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_plachetzki_EYS-5FPROM_issues_1&d=DwMCaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=gZl-jyQbfCQIs8dZ3FKCzwt0Dm_uEXeB_OX1lbaJOQs&m=UYm6HdKV6A2sDSM4As_fiej7L8YpmP51SazL0xKK6nk&s=0yBNEoejV1FqMTqAAmmG4sa_-xuey1qp23fh9W9HXts&e=, or mute the threadhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ANXcBdZZHpK4cquIYHstKnEwxA9HpZHOks5ugBC2gaJpZM4XAvn-2D&d=DwMCaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=gZl-jyQbfCQIs8dZ3FKCzwt0Dm_uEXeB_OX1lbaJOQs&m=UYm6HdKV6A2sDSM4As_fiej7L8YpmP51SazL0xKK6nk&s=K_m7Ic6BG1hF_LV9vcnqrhCvME8Ha3Wgip9kavihOk0&e=.