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[2022-03-08 10:23:36] INFO: Running: flye-minimap2 -ax asm5 -t 10 -K 5G <PATH>/assembly.fasta <PATH>/hapdup/flye_hap_1/polished_1.fasta 2>/dev/null | flye-samtools sort -m 4G -@4 > <PATH>/hapdup/structural/liftover_hp1.bam
[E::sam_parse1] missing SAM header
[W::sam_read1] Parse error at line 2
samtools sort: truncated file. Aborting
Traceback (most recent call last):
File "/usr/local/bin/hapdup", line 8, in <module>
sys.exit(main())
File "/usr/local/lib/python3.8/dist-packages/hapdup/main.py", line 245, in main
subprocess.check_call(" ".join(minimap_cmd), shell=True)
File "/usr/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'flye-minimap2 -ax asm5 -t 10 -K 5G <PATH>/assembly.fasta <PATH>/hapdup/flye_hap_1/polished_1.fasta 2>/dev/null | flye-samtools sort -m 4G -@4 > <PATH>/hapdup/structural/liftover_hp1.bam' returned non-zero exit status 1.
I suspect it could be because of the default minimap2 -I flag being too small (4G)?
If this is the case, maybe an option to specify this could be added, or adjust it automatically depending on genome size?
Thanks!
The text was updated successfully, but these errors were encountered:
Hi,
Ran into this error while trying to run hapdup:
I suspect it could be because of the default minimap2 -I flag being too small (4G)?
If this is the case, maybe an option to specify this could be added, or adjust it automatically depending on genome size?
Thanks!
The text was updated successfully, but these errors were encountered: