pangenome_matrix_genes_t0.tab is empty

[ireneortega]

I run get_homologues-x86_64-20210828/compare_clusters.pl -o sample_intersection -m -T -d gbk_homologues/*_f0_0taxa_algOMCL_e0_, but the file pangenome_matrix_genes_t0.tab is empty. I mean the ID for the gen in each genome is not included in that file, although the cluster names are present. The file pangenome_matrix_t0.tab correctly indicates the number of clusters per genome.

My GenBank files were created using PATRIC (.gb), perhaps this output is not suitable for get_homologues.

Here you cand find the log file: process.log

[eead-csic-compbio]

Hi @ireneortega , it might be that the gene accessions/names are not correctly parsed. Will you share with me those 3 gbk files to double-check? Thanks, Bruno

[ireneortega]

There you have 🙂

Thanks!

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De: eead-csic-compbio @.> Enviado: miércoles, 1 de diciembre de 2021 14:17 Para: eead-csic-compbio/get_homologues @.> Cc: IRENE ORTEGA SANZ @.>; Mention @.> Asunto: Re: [eead-csic-compbio/get_homologues] pangenome_matrix_genes_t0.tab is empty (Issue #86)

Hi @ireneortegahttps://github.com/ireneortega , it might be that the gene accessions/names are not correctly parsed. Will you share with me those 3 gbk files to double-check? Thanks, Bruno

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[eead-csic-compbio]

Sorry Irene, did not receive any attachment, can you perhaps paste here a URL so that I can download them? Bruno

[ireneortega]

I sent them to you attached by email. Sorry for the inconvenience. If you still can not download, I will try another way.

IRene

De: eead-csic-compbio @.> Enviado el: jueves, 2 de diciembre de 2021 17:08 Para: eead-csic-compbio/get_homologues @.> CC: IRENE ORTEGA SANZ @.>; Mention @.> Asunto: Re: [eead-csic-compbio/get_homologues] pangenome_matrix_genes_t0.tab is empty (Issue #86)

Sorry Irene, did not receive any attachment, can you perhaps paste here a URL so that I can download them? Bruno

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/eead-csic-compbio/get_homologues/issues/86#issuecomment-984770605, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN2Y6RF6YTICSVA57546TXTUO6KXLANCNFSM5JEJJS2Q. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[eead-csic-compbio]

Apparently attachments are not taken when you respond to these messages through your own email, please try a link, I'll have a look tomorrow

[eead-csic-compbio]

Hi @ireneortega , I have modified the code so that it parses correctly your gbk files (see details at https://github.com/eead-csic-compbio/get_homologues/commit/d0b6b2af46381adc98f67330b8511bc9c6c00788). Please git pull, remove your _homologues folder and re-run, Bruno

[ireneortega]

Worked perfectly! Thanks