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pianpianyouche / plascad

Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.
https://github.com/pianpianyouche/plascad
MIT License
45 stars 11 forks source link

Error: Failed to open sequence file example_MOB_temp_mob.faa for reading #3

Open szz65 opened 2 years ago

szz65 commented 2 years ago

Hi, @pianpianyouche I installed Plascad as you mentioned in the tutorial with conda environment. However, it will report an error when I ran Plascad with example.fasta or my own plasmids files.

Error: Sequence file example_MOB_temp_mob.faa is empty or misformatted

Error: Sequence file example_MOB_temp_mob.faa is empty or misformatted

cat: *ATPase.hmm_domtblout_parsed_out: No such file or directory
cat: *T4CP*_domtblout_parsed_out: No such file or directory
cat: example*MPFF*_result_out: No such file or directory
cat: example*MPFG*_result_out: No such file or directory
cat: example*MPFI*_result_out: No such file or directory
cat: example*MPFT*_result_out: No such file or directory
pianpianyouche commented 2 years ago

Hi, that's weird! I have tried to install this tool to different workstations, all work very well. Could you install it with pip? but you need to install the dependencies (Python >=3.6, blast >=2.7.1, prodigal >=2.6.3, hmmer >=3.2.1) in your PATH.

szz65 commented 2 years ago

I have tried to use Plascad on another server and it works very well. But when I install it with pip3 on the previous server, it reported the error again. I don't know what contributes to this problem... Could you please provide a docker image for Plascad? Thanks! @pianpianyouche