{"action":"created","issue":{"url":"https://api.github.com/repos/merenlab/anvio/issues/759","repository_url":"https://api.github.com/repos/merenlab/anvio","labels_url":"https://api.github.com/repos/merenlab/anvio/issues/759/labels{/name}","comments_url":"https://api.github.com/repos/merenlab/anvio/issues/759/comments","events_url":"https://api.github.com/repos/merenlab/anvio/issues/759/events","html_url":"https://github.com/merenlab/anvio/issues/759","id":300780344,"number":759,"title":"`--concatenate-gene-clusters` produces a _mostly_ empty file","user":{"login":"ekiefl","id":8688665,"avatar_url":"https://avatars3.githubusercontent.com/u/8688665?v=4","gravatar_id":"","url":"https://api.github.com/users/ekiefl","html_url":"https://github.com/ekiefl","followers_url":"https://api.github.com/users/ekiefl/followers","following_url":"https://api.github.com/users/ekiefl/following{/other_user}","gists_url":"https://api.github.com/users/ekiefl/gists{/gist_id}","starred_url":"https://api.github.com/users/ekiefl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekiefl/subscriptions","organizations_url":"https://api.github.com/users/ekiefl/orgs","repos_url":"https://api.github.com/users/ekiefl/repos","events_url":"https://api.github.com/users/ekiefl/events{/privacy}","received_events_url":"https://api.github.com/users/ekiefl/received_events","type":"User","site_admin":false},"labels":[{"id":82726073,"url":"https://api.github.com/repos/merenlab/anvio/labels/bug","name":"bug","color":"fc2929","default":true},{"id":781329558,"url":"https://api.github.com/repos/merenlab/anvio/labels/phylogenomic%20workflow","name":"phylogenomic 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on the pangenome in the metapangenomics paper, when the above flag is provided the gene sequences are empty and the file looks like this:\r\n\r\n`anvi-get-sequences-for-gene-clusters --report-DNA-sequences -p Prochlorococcus-PAN-PAN.db -g Prochlorococcus-PAN-GENOMES.db -o concatenated_alignment.fa --min-num-genomes-gene-cluster-occurs 31 --max-num-genes-from-each-genome 1 --concatenate-gene-clusters --align-with muscle`\r\n\r\n```\r\nMode .........................................: Reporting alignments for all gene clusters.\r\nGenomes storage .............................................: Initialized (storage hash: fed45e7c)\r\nNum genomes in storage ......................................: 31\r\nNum genomes will be used ....................................: 31\r\nPan DB ......................................................: Initialized: Prochlorococcus-PAN-PAN.db (v. 8)\r\n\r\n* Gene clusters are initialized for all 7386 gene clusters in the database.\r\n\r\n\r\nGENE CLUSTER FILTERS\r\n==============================================================\r\nBased on --min-num-genomes-gene-cluster-occurs 31, --max-num-genomes-gene-\r\ncluster-occurs 31, --min-num-genes-from-each-genome 0, and --max-num-genes-from-\r\neach-genome 1 (some of these may be default values, no need to panic).\r\n\r\nAll gene clusters (7386) ....................................: GC_00003471, GC_00007224, GC_00002325, (... 7383 more (`--debug` will show all))\r\nGene clusters that passed the filter (660) ..................: GC_00000659, GC_00000645, GC_00000249, (... 657 more (`--debug` will show all))\r\nGenes clusters that filed the filter (6726) .................: GC_00003471, GC_00007224, GC_00002325, (... 6723 more (`--debug` will show all))\r\n\r\nSequence type ...............................................: DNA\r\nOutput file for phylogenomics ...............................: concatenated_alignment.fa\r\n```\r\n\r\n```\r\n>AS9601\r\n\r\n>CCMP1375\r\n\r\n>EQPAC1\r\n\r\n>GP2\r\n\r\n>LG\r\n\r\n>MED4\r\n\r\n>MIT9107\r\n\r\n>MIT9116\r\n\r\n>MIT9123\r\n\r\n>MIT9201\r\n\r\n>MIT9202\r\n\r\n>MIT9211\r\n\r\n>MIT9215\r\n\r\n>MIT9301\r\n\r\n>MIT9302\r\n\r\n>MIT9303\r\n\r\n>MIT9311\r\n\r\n>MIT9312\r\n\r\n>MIT9313\r\n\r\n>MIT9314\r\n\r\n>MIT9321\r\n\r\n>MIT9322\r\n\r\n>MIT9401\r\n\r\n>MIT9515\r\n\r\n>NATL1A\r\n\r\n>NATL2A\r\n\r\n>PAC1\r\n\r\n>SB\r\n\r\n>SS2\r\n\r\n>SS35\r\n\r\n>SS51\r\n\r\n```\r\n\r\n--------------------------------\r\n\r\nwhen I run the same command without the flag it produces the following log and the output file looks like it's supposed to:\r\n\r\n```\r\nMode .........................................: Reporting alignments for all gene clusters.\r\nGenomes storage .............................................: Initialized (storage hash: fed45e7c)\r\nNum genomes in storage ......................................: 31\r\nNum genomes will be used ....................................: 31\r\nPan DB ......................................................: Initialized: Prochlorococcus-PAN-PAN.db (v. 8)\r\n\r\n* Gene clusters are initialized for all 7386 gene clusters in the database.\r\n\r\n\r\nGENE CLUSTER FILTERS\r\n==============================================================\r\nBased on --min-num-genomes-gene-cluster-occurs 31, --max-num-genomes-gene-\r\ncluster-occurs 31, --min-num-genes-from-each-genome 0, and --max-num-genes-from-\r\neach-genome 1 (some of these may be default values, no need to panic).\r\n\r\nAll gene clusters (7386) ....................................: GC_00001203, GC_00004587, GC_00001891, (... 7383 more (`--debug` will show all))\r\nGene clusters that passed the filter (660) ..................: GC_00000554, GC_00000205, GC_00000443, (... 657 more (`--debug` will show all))\r\nGenes clusters that filed the filter (6726) .................: GC_00001203, GC_00004587, GC_00001891, (... 6723 more (`--debug` will show all))\r\n\r\nSequence type ...............................................: DNA\r\nNum sequences reported ......................................: 20,460\r\nOutput FASTA file ...........................................: concatenated_alignment.fa\r\n```"},"comment":{"url":"https://api.github.com/repos/merenlab/anvio/issues/comments/369619636","html_url":"https://github.com/merenlab/anvio/issues/759#issuecomment-369619636","issue_url":"https://api.github.com/repos/merenlab/anvio/issues/759","id":369619636,"user":{"login":"ekiefl","id":8688665,"avatar_url":"https://avatars3.githubusercontent.com/u/8688665?v=4","gravatar_id":"","url":"https://api.github.com/users/ekiefl","html_url":"https://github.com/ekiefl","followers_url":"https://api.github.com/users/ekiefl/followers","following_url":"https://api.github.com/users/ekiefl/following{/other_user}","gists_url":"https://api.github.com/users/ekiefl/gists{/gist_id}","starred_url":"https://api.github.com/users/ekiefl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekiefl/subscriptions","organizations_url":"https://api.github.com/users/ekiefl/orgs","repos_url":"https://api.github.com/users/ekiefl/repos","events_url":"https://api.github.com/users/ekiefl/events{/privacy}","received_events_url":"https://api.github.com/users/ekiefl/received_events","type":"User","site_admin":false},"created_at":"2018-03-01T15:03:09Z","updated_at":"2018-03-01T15:03:09Z","author_association":"CONTRIBUTOR","body":"> how about running it with this instead: --align-with famsa --concatenate\r\n\r\nsame thing"}}
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