Comments (5)
WillCh07
commented on September 26, 2024
How did you get the "collapsed.sorted.gff" from the SMRT Link, did you use the same reference?
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yesh1m
commented on September 26, 2024
They got the file from output directory of SMRTLink by using the same reference FASTA file from Ensembl.
Also, they tried the analysis via command line started from hifi.bam but encountered same issue.
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WillCh07
commented on September 26, 2024
Have they checked their analysis status, like ram usage (htop), it looks like there are too many scaffolds and contigs to accomplish the analysis.
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yesh1m
commented on September 26, 2024
Yes, after certain JH#, the process disappears without any message. Do you think specifying the number of threads to use via the '-j' option might address this issue?
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armintoepfer
commented on September 26, 2024
We can't help you with data processing. If you provide a small reproducible test case, we can have a look. Closing until reproducible case is available.
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Related Issues (20)
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