Christian Edwardson

I just had this issue as well. Giving CheckM a directory rather than a single FASTA file solved it!

OK. I think this has something to do with my dataset. The headers of the BAM files and the contigs are "SPAdes"-style but "fixed" with sed and samtools to be...

I believe the problem is that my reads are single reads, not paired end. Example output: [2018-02-06 23:08:18] INFO: Calculating coverage profile for 31b_SL115863_0_trimmed.sorted.bam (10 of 10): Finished processing 355358...

OK that worked, but the error in refinem outliers did not disappear. [2018-02-07 23:33:01] INFO: RefineM v0.0.23 [2018-02-07 23:33:01] INFO: refinem outliers coverage_stats_new_bins/scaffold_stats.tsv bin_outliers_new_bins [2018-02-07 23:33:01] INFO: Reading scaffold statistics....

I've sent you a Google drive link since its 91MB compressed.

Hi, I'm just getting back to this problem. I'm still getting the error after exploring some things as described below. First, these bins were from 10 samples, 5 depths in...

OK. Thanks!

Reopening this issue, but also this is sort of a follow up to #11. After removing the zero-coverage contigs, remapping, and recalculating scaffold stats, as well as removing single contig...