Can CoverM contig be run in batches?

[try-hunter]

Hi, when I use coverm contig --methods metabat --bam-files, I run out of memory because there are too many BAM files. I'm wondering if it's feasible to complete the process by running in batches and then merging the files. Will this approach lead to any deviations from the results obtained by running all files at once?

[wwood]

Hi, Yes, you can simply combine the TSV results and you would get the same thing. Another option is to use the output format sparse, which from memory would output using less ram. But then you'd need to convert back to dense format if you wanted to feed that into the meta at program. Hth, ben -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

…

________________________________ From: try-hunter ***@***.***> Sent: Sunday, August 3, 2025 9:31:32 PM To: wwood/CoverM ***@***.***> Cc: Subscribed ***@***.***> Subject: [wwood/CoverM] Can CoverM contig be run in batches? (Issue #264) [https://avatars.githubusercontent.com/u/62093425?s=20&v=4]try-hunter created an issue (wwood/CoverM#264)<#264> Hi, when I use coverm contig --methods metabat --bam-files, I run out of memory because there are too many BAM files. I'm wondering if it's feasible to complete the process by running in batches and then merging the files. Will this approach lead to any deviations from the results obtained by running all files at once? ― Reply to this email directly, view it on GitHub<#264>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5AWCWIF7GOZEFX5PQL3LXXJJAVCNFSM6AAAAACC734OIGVHI2DSMVQWIX3LMV43ASLTON2WKOZTGI4DOMBZGM3DSOA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>