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bartongroup / Simpson_Barton_Nanopore_1

jupyter notebooks for Parker et al. eLife 2019
MIT License
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Request to open the ORFfinder module under chimera_pieline #3

Closed weir12 closed 4 years ago

weir12 commented 4 years ago

Hi: An error occurred when I ran the following rule. https://github.com/bartongroup/Simpson_Barton_Nanopore_1/blob/1b509454a9e25a8c81be5092f8e525ca00e7b5a5/pipeline/chimera_pipeline/Snakefile#L103 error msg: /usr/bin/bash: scripts/ORFfinder: No such file or directory

So I request that this executable be made public, If you don't mind :) Thanks again! weir

mparker2 commented 4 years ago

Orf finder is available from the NCBI website. ftp://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/linux-i64/

weir12 commented 4 years ago

Thanks Have you ever encountered this problem？

Error (1478537b-fce6-4c76-8b3a-130fac30c2fe::Mt:360821-363129(-)) :
 CFastaReader: Near line 1, the local id is too long.  Its length is 57 but the maximum allowed local id length is 50.  
Please find and correct all local ids that are too long.

Can I clip the Sequence Tag to a legal length in {sample}. Chimera_seqs.bed ?

mparker2 commented 4 years ago

seems to be to do with differences in the length of the fasta record id produced by bedtools getfasta with different bedtools versions, see https://github.com/arq5x/bedtools2/issues/609

If you are using bedtools < 2.27, you can just trim the fasta record id as you say. Or update to 2.27.1 which should produce shorter record ids.

weir12 commented 4 years ago

Thanks,problem was resolved by downgrading bedtools to v.2.27