DIAMOND as no option --query

[iquasere]

Greetings

I have been trying to use your tool, and a problem arose in the FMAP_assembly.pl part of the workflow.

diamond: error: no such option: --query
ERROR in FMAP_assembly.pl: readline() on closed filehandle $reader at FMAP_assembly.pl line 283.

I compiled FMAP as it is suggested, and DIAMOND was installed as follows:

wget http://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz
sudo apt-get install python-configobj

Since I have used DIAMOND before without such errors, I have no idea what is going on here. I did associated FMAP with the DIAMOND binary that so far gave me no errors.

Thank you for your attention

[jiwoongbio]

Thanks for your interest in FMAP_assembly. Can you please try again with specifying the path of diamond executable using the option "-m" of FMAP_assembly.pl.

On Wed, Jul 11, 2018 at 10:13 AM, João Sequeira notifications@github.com wrote:

Greetings

I have been trying to use your tool, and a problem arose in the FMAP_assembly.pl part of the workflow.

diamond: error: no such option: --query ERROR in FMAP_assembly.pl: readline() on closed filehandle $reader at FMAP_assembly.pl line 283.

I compiled FMAP as it is suggested, and DIAMOND was installed as follows:

wget http://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz tar xzf diamond-linux64.tar.gz sudo apt-get install python-configobj

Since I have used DIAMOND before without such errors, I have no idea what is going on here. I did associated FMAP with the DIAMOND binary that so far gave me no errors.

Thank you for your attention

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[iquasere]

Thank you for the quick answer, it did solved the DIAMOND problem. But outing to summary.txt gives a file with no content. Why?

[iquasere]

This is the "FMAP_assembly.abundance.txt" file used in the FMAP_assembly_heatmap step right?

[jiwoongbio]

Yes. The file is the final output.

On Tue, Jul 17, 2018 at 12:54 PM, João Sequeira notifications@github.com wrote:

This is the "FMAP_assembly.abundance.txt" file used in the FMAP_assembly_heatmap step right?

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[iquasere]

Besides the problem with the summary.txt empty file, I have now another question: I have been testing the tool through the second route here exposed, using a MG paired end dataset, and 3 MT datasets, one control and two other conditions. In the step of "FMAP_comparison.pl", I input data as such:

perl FMAP_comparison.pl path/to/abundance_table.txt path/to/MT1_forward.fastq,path/to/MT1_reverse.fastq path/to/MT2_forward.fastq,path/to/MT2_reverse.fastq path/to/MT3_forward.fastq,path/to/MT3_reverse.fastq   > orthology_test_stat.txt

and it outputs

ERROR in FMAP_comparison.pl: The comparison requires at least 3 samples per group.

Why is that? How should I input the arguments?

[iquasere]

I only used the MG dataset for the previous steps, thinking FMAP would identify the genes present, and then align the MT data to it to detect gene expression. Do I have to put the MT data right from the start?

[jiwoongbio]

I am sorry for the late reply. You can input MT for gene expression analysis, but the original idea of the function is to estimate gene abundances influenced by taxonomic abundances and copy numbers. Thanks.

Best Regards, Jiwoong