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BUG: Indexing of Spur_5.0 assembly fails #436
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This happens with immature genomes/annotations. I suggest sticking with the older assembly for a while longer, but we could make the function "skip groups with errors" using flag |
What would that do? I guess in my case I would prefer it to ignore the annotation, since the alignment is more important than the annotation visualization in the ucsc trackhub |
Since the rule is trackhub_index, I guess that any genes on that contig are unsearchable on UCSC. |
I don't know if that is what you proposed. What would -allErrors do? |
I think it means it just skips the lines in the annotation that cause an error. |
Spur_5.0 has different contig names in the genome fasta and the annotation. NCBI will have to fix this, or you must manually change them :( |
I would like to keep this one open (at least for now), until I have a solution for myself |
Describe the bug
When making an index for assembly Spur_5.0 rule trackhub_index fails:
NC_001453.1 is not found in chromosome sizes file
To Reproduce
I ran the atac-seq pipeline with many samples, but I guess this should be enough to reproduce:
Expected behavior
No failure! Is this a genomepy+annotation thingy? Or is it on our side?
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