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friend1ws / nanomonsv

SV detection tool for nanopore sequence reads
GNU General Public License v3.0
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nanomonsv insert_classify: Executable does not exist: minimap2 #24

Closed charliechen912ilovbash closed 1 year ago

charliechen912ilovbash commented 2 years ago

I am using v0.4.0. My command is: nanomonsv insert_classify --genome_id hg38 and it results in: nanomonsv.utils - ERROR - Executable does not exist: minimap2 But I have installed the minimap2 with conda and it can be called by minimap2 in shell, so I am not sure which part is going wrong..

friend1ws commented 1 year ago

Sorry for the late response. nanomonsv insert_classify calls minimap2 through subprocess.check_call. So I guess it would not be a problem.. One way to check is to try simple script such as

# /usr/bin/env ptyhon3

import subprocess

input_fasta = sys.argv[1]
output_sam = sys.argv[2]
reference = sys.argv[3]

with open(output_sam, 'w') as hout:
    subprocess.check_call(["minimap2", "-ax", "splice", reference, input_fasta], stdout = hout)

And see what's happens?