Indexcov errors

[emmakwiener]

Hi @brentp I have been trying to run Indexcov on a directory of bams using this command goleft indexcov --directory /spaces/emma/goleft/Results /dataJ/build38/datasets/baylor/combined_bams/*.bam and I am getting the following errors..this is just a few lines....there were thousands of these lines 2020/09/25 16:43:50 no reference stats found for 66th reference 2020/09/25 16:43:50 no reference stats found for 76th reference 2020/09/25 16:43:50 no reference stats found for 78th reference 2020/09/25 16:43:50 no reference stats found for 81th reference 2020/09/25 16:43:50 no reference stats found for 112th reference 2020/09/25 16:43:50 no reference stats found for 115th reference etc. etc. What could be causing this?

[brentp]

Hi. it's likely OK with those messages. It just means that there were no alignments to those contigs/chroms, they are likely small un placed chromosomes or decoys. I should probably hide those messages for very small chromosomes....

[brentp]

Does this answer your question? There should still be the html output...