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meglab-metagenomics / amrplusplus_v2

MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data
http://megares.meglab.org/
MIT License
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snp_confirmation.py absents #13

Open VoronDM opened 4 years ago

VoronDM commented 4 years ago

I find in nextflow.config:

    /* Location of SNP confirmation script */
    snp_confirmation = "bin/snp_confirmation.py"

But there are no file snp_confirmation.py in /bin and nowhere

I see such output when using testing data:

[ab/0354ae] process > SNPconfirmation (S3_test)                       [100%] 3 of 3, failed: 3 ✔
[-        ] process > Confirmed_AMR_hits                              -
[f6/105481] process > Confirmed_ResistomeResults (null)               [100%] 1 of 1, failed: 1 ✔
[36/3101e4] process > ExtractDedupSNP (S3_test)                       [100%] 3 of 3 ✔
[84/90e800] process > RunDedupRGI (S3_test)                           [100%] 3 of 3 ✔
[91/322d1f] process > DedupSNPconfirmation (S3_test)                  [100%] 3 of 3, failed: 3 ✔
[-        ] process > ConfirmDedupAMRHits                             -
[81/aec48e] process > DedupSNPConfirmed_ResistomeResults (null)       [100%] 1 of 1, failed: 1 ✔

_Originally posted by @VoronDM in https://github.com/meglab-metagenomics/amrplusplus_v2/issues/12#issuecomment-715335809_