Michael Alonge
Michael Alonge
@xiekunwhy I checked your AGP files and I could not find anything obviously wrong. Do you mind opening up a separate issue? Please provide the following aside from the AGP...
Hi there, It all really comes down to the alignments. I suggest you run with `--debug` and you can compare the alignments for particular contigs across the different paf files....
Hi there, I am open to this though I would need someone else to contribute since I no longer have time for much development. I will leave this issue open...
Hi there, At a glance, it looks like the AGP file is incorrectly formatted (perhaps compressed?). Can you delete `ragtag.scaffolds.agp` and try it again? Thanks
Thanks for trying that. I can't quite think of what might be going on. Basically, pysam is just trying to read the query assembly. sequence but it is getting bytes...
Hi there, Thanks for sharing the data. It is strange that the sequences are written as bytes. Unfortunately, I was unable to reproduce the error on my end. Perhaps you...
Hi there, At a glance, this appears to happen when there are sequences with no restriction fragment sites. I'll leave this issue open as a bug because the software should...
Hi there, Sorry about the late reply. Can you run the following command and share the output? `grep ^"COV" c_reads_against_query.s.bam.stats`
Hi there, I would disregard #21. This shouldn't be influenced by the size of the alignment file. Could you provide the list of the reference and target assembly sequence headers?...
My first guess is that you have multiple sequences with the same header in your fasta files. Please check that and let me know.