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MinPath.py error

Open ndmrsn opened this issue 4 years ago • 2 comments

Getting this output after running for a few hours:

[Fri Jan 29 12:54:11 2021] ******start running minpath MinPath.py -ko $HOME/metaerg_01-29-2021/data/cds.gene2ko.mapping.txt -report $HOME/metaerg_01-29-2021/data/cds.gene2ko.minpath -details $HOME/metaerg_01-29-2021/data/cds.gene2ko.minpath.details > /dev/null 2>&1;

[Fri Jan 29 12:54:11 2021] Running: MinPath.py -ko $HOME/metaerg_01-29-2021/data/cds.gene2ko.mapping.txt -report $HOME/metaerg_01-29-2021/data/cds.gene2ko.minpath -details $HOME/metaerg_01-29-2021/data/cds.gene2ko.minpath.details > /dev/null 2>&1;

[Fri Jan 29 12:54:11 2021] Could not run command:MinPath.py -ko $HOME/T3MP1/metaerg_01-29-2021/data/cds.gene2ko.mapping.txt -report $HOME/metaerg_01-29-2021/data/cds.gene2ko.minpath -details $HOME/metaerg_01-29-2021/data/cds.gene2ko.minpath.details > /dev/null 2>&1;, No such file or directory

[Fri Jan 29 12:54:14 2021] Could not run command:/usr/bin/perl $HOME/metaerg/bin/output_reports.pl -g $HOME/metaerg_01-29-2021/data/all.gff -o $HOME/metaerg_01-29-2021 -f $HOME/metaerg_01-29-2021/metaerg.pl_01292021.fna,

ndmrsn avatar Jan 29 '21 18:01 ndmrsn

Getting this output: Sat Jan 30 18:55:58 2021] ******start running minpath MinPath.py -ko test1/data/cds.gene2ko.mapping.txt -report test1/data/cds.gene2ko.minpath -details test1/data/cds.gene2ko.minpath.details > /dev/null 2>&1;

[Sat Jan 30 18:55:58 2021] Running: MinPath.py -ko test1/data/cds.gene2ko.mapping.txt -report test1/data/cds.gene2ko.minpath -details test1/data/cds.gene2ko.minpath.details > /dev/null 2>&1; [Sat Jan 30 18:55:58 2021] Could not run command:MinPath.py -ko test1/data/cds.gene2ko.mapping.txt -report test1/data/cds.gene2ko.minpath -details test1/data/cds.gene2ko.minpath.details > /dev/null 2>&1;, No such file or directory

[Sat Jan 30 18:56:08 2021] Could not run command:/media/jaca/scratch/programs/metaerginstall/bin/perl /media/jaca/scratch/programs/metaerginstall/metaerg/bin/output_reports.pl -g test1/data/all.gff -o test1 -f test1/metaerg.pl_01302021.fna,

jacarcher avatar Jan 30 '21 21:01 jacarcher

I also encountered the same problem. In my case, the python script I installed is called MinPath1.4.py but not MinPath.py. Can solve it by renaming the script or changing it in output_reports.pl.

niccw avatar Feb 14 '21 15:02 niccw