Samuel Aroney

No. They were as expected

Yes, `coverm_abundances.tsv` is indeed empty. Also, `coverm.cov`, `coverm.filt.cov`, `long_abundances.tsv`, `long_cov.tsv` and `short_cov.tsv` are not empty. But `short_abundances.tsv` is empty.

Yes, `coverm.cov` does have short read information. I can't see any error information for get_abundances. ``` [Fri Oct 14 06:31:13 2022] rule get_abundances: input: bins/checkm.out output: data/coverm_abundances.tsv jobid: 25 reason:...

I've done 18 assemblies (6 each of long-only, long+short, short-only). All 10 that have finished recover so far have this error.

I haven't tried with only long or only short yet but I can give that a go. ``` job count min threads max threads --------------------- ------- ------------- ------------- checkm2 1...

Oh I mean that the assemblies were done with short, long, short+long but that the recovery was done with the same samples (for comparison). So recovery was always done with...

This happened again with only short-reads. I noticed that the real error is `ERROR coverm::bam_generator] Not continuing since when input file pairs have unequal numbers of reads this usually means...

The order of short_reads_2 in the config doesn't match that of short_reads_1 and neither match the order in the initial command.

Might be due to the set() conversion from commit 4eaefb4b35faec0d77cfa3979f44212227cb7d40

Do you have plans to revisit this? Looks like the pull-request stalled (https://github.com/bioconda/bioconda-recipes/pull/29099).