Comments (3)
colindaven
commented on June 15, 2024
Hi @Colorstorm can you please report this if not yet known to the sambamba developers ? It happens when we try to align to a de novo reference genome.
Thanks
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colindaven
commented on June 15, 2024
- test using samtools to remove dups, now multicore
Need to find another tool for markdup. This error torpedoes use of more than 16K reference sequence, eg de novo assemblies, also the new massive ref sequences. Alignment is fine but it crashes on the sambamba markdup step.
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colindaven
commented on June 15, 2024
Completed using samtools for markdup in 1.7.7 9459fff
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