Hi, when running METABOLIC-C (either test or my data), it fails to create the All_gene_collections.gene file, and all the downstream mapping fails. After "Drawing element cycling diagrams..." it states "No output file specified!". Please help - many thanks in advance!

[MaxRubinBlum]

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[ChaoLab]

Hi, It can be due to some dependencies are not well-installed. Were the gene files generated in the genome folder? The "All_gene_collections.gene" is the concatenated file from gene files in the genome folder.

[MaxRubinBlum]

Yes, the gene files were generated.

[MaxRubinBlum]

Hi, thanks for the response! Still cannot make this work. I tried to override this by concatenating the files manually and re-running the script, but the file apparently gets removed, and the issue still remains. Bowtie 2 thus fails to build an index. I am running a manual installation, as my conda is quite broken and fails to build environments due to conflict issues. I think all the dependencies were installed. What am I missing? Thanks for the help.

[ChaoLab]

It will be much easier to run within conda since there are many dependencies

[MaxRubinBlum]

I understand, but this is not feasible at the moment. Which dependency could be missing to cause this issue?

[MaxRubinBlum]

Dear Zhichao,

I am still having a problem resolving this issue, your help is highly appreciated.

Many thanks, Maxim

From: Zhichao Zhou @.> Sent: Saturday, 12 March 2022 21:37 To: AnantharamanLab/METABOLIC @.> Cc: Maxim Rubin Blum @.>; Author @.> Subject: Re: [AnantharamanLab/METABOLIC] Hi, when running METABOLIC-C (either test or my data), it fails to create the All_gene_collections.gene file, and all the downstream mapping fails. After "Drawing element cycling diagrams..." it states "No output file ...

It will be much easier to run within conda since there are many dependencies

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[ChaoLab]

Can you try to use Bowtie2 to make the index independent of the METABOLIC? Maybe you can also try to run the following Bowtie2 mapping steps for troubleshooting. Sometimes, it could be just a dependency issue

[H1889]

Hi, I have had the same problem and I think it is an error of the perl script "METABOLIC-C.pl". The line 1904 is:

system ("bowtie2-build $output/All_gene_collections.gene $output/All_gene_collections.gene.scaffold --quiet");

but must be written:

system ("bowtie2-build --quiet $output/All_gene_collections.gene $output/All_gene_collections.gene.scaffold");

The bowtie2 manual says: Usage: bowtie2-build [options]*

so the options must be written BEFORE the reference and base name not AFTER.

Best regards

[ChaoLab]

@H1889 Hi, I changed the script accordingly

[patriciatran]

Hi @MaxRubinBlum , have you been able to test with our updates METABOLI-c.pl scripts (see comments above) ? Thanks for letting us know.

[MaxRubinBlum]

Hi @patriciatran, not yet, will certainly give it a go. Many thanks!

[H1889]

I tested it and worked, however this error does not: ...: [2022-04-10 01:00:51] Drawing element cycling diagrams finished [2022-04-10 01:00:51] Drawing metabolic handoff diagrams... mv: no se puede efectuar stat' sobre 'COMMUNITY_BACTERIA_OUT/newdir/Bar_plot/bar_plot_input_1.pdf'mv: no se puede efectuarstat' sobre 'COMMUNITY_BACTERIA_OUT/newdir/Bar_plot/bar_plot_input_1.pdf': No existe el archivo o el directorio : No existe el archivo o el directorio mv: no se puede efectuar stat' sobre 'COMMUNITY_BACTERIA_OUT/newdir/Bar_plot/bar_plot_input_2.pdf'mv: no se puede efectuarstat' sobre 'COMMUNITY_BACTERIA_OUT/newdir/Bar_plot/bar_plot_input_2.pdf': No existe el archivo o el directorio : No existe el archivo o el directorio ....