DioufMouss0 commented 4 months ago

Hello, I have made my analysis with SqueezeMeta and now I want to move further using the sqm2itol.pl but I am having this error message. could you please help with this?

Thanks

sqm2itol.pl EBFGSQM2 Reading bins in /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/results/18.EBFGSQM2.bintable... Found bins Working with bins with more than 30% completion and less than 100% contamination Using RPKM values Reading functions in /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/results/21.EBFGSQM2.metacyc.pathways Died at /home/abk/miniconda3/envs/Squeezemeta/bin/sqm2itol.pl line 147.

jtamames commented 4 months ago

Hello Please see my responses to this issue in #798 . Best, J

DioufMouss0 commented 4 months ago

Here Sir and thank you for your reply; i have made the changes you suggested and that error disapeared. however another one has came related to comparem.

find the details:

Reading bins in /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/results/18.EBFGSQM2.bintable... Found bins Working with bins with more than 30% completion and less than 100% contamination Using RPKM values Reading functions in /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/results/20.EBFGSQM2.metacyc.pathways Reading sequences in /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/results/03.EBFGSQM2.faa

Running CompareM: PATH=/home/abk/Desktop/Array/Metagenomics/NGS_tools/SqueezeMeta/bin:$PATH comparem aai_wf --proteins /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/temp/comparem -x faa /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/results/bins [2024-02-27 20:40:23] INFO: CompareM v0.0.23 [2024-02-27 20:40:23] INFO: comparem aai_wf --proteins /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/temp/comparem -x faa /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/results/bins [2024-02-27 20:40:23] WARNING: No genomes found in directory: /media/abk/T71/Metagenomics_UM6P/data_analysis/MetaGenome/EBFGSQM2/temp/comparem. Check the --file_ext flag used to identify genomes.

Controlled exit resulting from an unrecoverable error or warning. Died at /home/abk/miniconda3/envs/Squeezemeta/SqueezeMeta/utils/sqm2itol.pl line 249.

jtamames commented 4 months ago

Hello Did you follow all the instructions? Including this one?

Comment line 105:
# next if($k[1] ne "DASTool"); 
Change line 145 to:
my $funfile="$resultpath/20.$project.$funclass.pathways";

DioufMouss0 commented 4 months ago

Yes, I made the modifications you proposed.

I think this error is related to the comparem when I checked the comparem folder there were no file and when I copy the genome file to that folder it disappears when the analysis start.

Aliou

From: Javier Tamames @.> Sent: Wednesday, February 28, 2024 10:32:31 AM To: jtamames/SqueezeMeta @.> Cc: Diouf Moussa @.>; Author @.> Subject: Re: [jtamames/SqueezeMeta] sqm2itol.pl Died at sqm2itol.pl line 147. (Issue #800)

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Hello Did you follow all the instructions? Including this one?

Comment line 105:

next if($k[1] ne "DASTool");

Change line 145 to: my $funfile="$resultpath/20.$project.$funclass.pathways";

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DioufMouss0 commented 4 months ago

Hi Professor, any update regarding this issue?

jtamames commented 4 months ago

The problem is that the script is not finding any bins. If you did all the modifications as suggested, it could be that you do not have any bins from a start. Did you check that?

DioufMouss0 commented 4 months ago

Hi Professor, thank you for your response the tree is generating now I forgot to include the # in line 105.

thanks

fpusan commented 2 months ago

Closing due to lack of activity, feel free to reopen

jtamames / SqueezeMeta

sqm2itol.pl Died at sqm2itol.pl line 147. #800

next if($k[1] ne "DASTool");