skoren
commented
1 year ago I'm not sure I understand what you're trying to do with the downsampling. You're keeping only reads shorter than some threshold for the same dataset as the successful run? If so, 10kb input that failed has only 27 reads and is less than 1x of coverage of the 5mb genome so I think the issue is no reads are left to correct. If the sets w/8 and 4kb thresholds have even fewer reads to correct, then they would be failing for the same reason.
Hollowed-Mind
brianwalenz
I can run the canu program successfully using two different fastqs of 20x reads from 5,160,000 base pairs, but the second I try running it with reads from smaller sequences it fails in the correction step.
I've tried it with 20x coverage reads from 10,000bp, 8000bp and ~4000bp. All fail in the same step.
Attached are two records from my terminal. One where canu finished the program (from one of two fastq reads from a 5,160,000 bp sample) and one record where canu stalled and aborted (when I tried to use it to assemble reads from a 10,000bp sequence).
What do you think is going on here?
failed_canu_run_record.txt successful_canu_run_record.txt