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jotech / gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
GNU General Public License v3.0
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transporter prediction leads to a zerobytes Transporter.tbl result #223

Open Lishijiagg opened 6 days ago

Lishijiagg commented 6 days ago

for bug reports and errors please report the output of: ./gapseq test Hi, First of all thanks for such a excellent work of gapseq. When I tried to reconstruct a metabolic network from a genome of B.fragilis, the command ./gapseq find-transport bfragilis/GCF_016889925.1_ASM1688992v1_genomic.fna.gz leads to a null Transporter.tbl file. What might be the cause of this problem?

Lishijiagg commented 6 days ago

here is the information of this command:

(base) lishijia@lishijiadeMacBook-Pro gapseq % ./gapseq find-transport /Users/lishijia/gapseq/bbreve/GCF_001025175.1_ASM102517v1_genomic.fna.gz Nucleotide fasta detected. sed: 1: "fasta_header": invalid command code f sed: 1: "fasta_header": invalid command code f grep: invalid option -- P usage: grep [-abcdDEFGHhIiJLlMmnOopqRSsUVvwXxZz] [-A num] [-B num] [-C[num]] [-e pattern] [-f file] [--binary-files=value] [--color=when] [--context[=num]] [--directories=action] [--label] [--line-buffered] [--null] [pattern] [file ...]

Found transporter for substances:

Found transporter without reaction in DB: Total number of found substance transporter for GCF_001025175.1_ASM102517v1_genomic: 0 stat: illegal option -- c usage: stat [-FLnq] [-f format | -l | -r | -s | -x] [-t timefmt] [file ...] sed: 1: "/Users/lishijia/gapseq/ ...": extra characters at the end of l command sed: 1: "/Users/lishijia/gapseq/ ...": extra characters at the end of l command Running time: 168 s.

Waschina commented 5 days ago

Could you report the output of ./gapseq test?