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Maggi-Chen / Inspector

A tool for evaluating long-read de novo assembly results
MIT License
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minimap2: command not found #13

Open mergi-2674 opened 1 year ago

mergi-2674 commented 1 year ago

Hi Maggi, I was running Inspector on the assembled genome on a cluster node with 128 Gb of ram and 48 threads, I installed all the dependencies and run Inspector. However after running for a while it crushed a couple of times and gave me the same error.

"sh: minimap2: command not found samtools sort: failed to read header from "-" mv: cannot stat ‘/STORAGE/DATA/xxx/xxxx/flye_assembly/read_to_contig_1.bam’: No such file or directory [E::hts_open_format] Failed to open file "//STORAGE/DATA/xxx/xxxx/Ins_flye_assembly/read_to_contig.bam" : No such file or directory samtools index: failed to open "/STORAGE/DATA/xxx/xxxx/Ins_flye_assembly/read_to_contig.bam": No such file or directory cat: /STORAGE/DATA/xxx/xxxx/Ins_flye_assembly/debreak_workspace/read_tocontig*debreak.temp: No such file or directory Traceback (most recent call last): File "/home/apps/user_apps/xxx/xxx_apps/Inspector/inspector.py", line 131, in cov=denovo_static.mapping_info_ctg(denovo_args.outpath,chromosomes_large,chromosomes_small,totalcontiglen,totalcontiglen_large) File "/home/apps/user_apps/piwczyn/mergi_apps/Inspector/denovo_static.py", line 123, in mapping_info_ctg unmapped=int(pysam.AlignmentFile(outpath+'read_to_contig.bam','rb').unmapped) File "pysam/calignmentfile.pyx", line 318, in pysam.calignmentfile.AlignmentFile.cinit (pysam/calignmentfile.c:4730) File "pysam/calignmentfile.pyx", line 534, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:7261) IOError: file //STORAGE/DATA/xxx/xxxx/Ins_flye_assembly/read_to_contig.bam not found "

How should it get fixed?

Thanks ,

Maggi-Chen commented 1 year ago

Hello Mergi,

I think the major problem is that “minimap2” was not found, so the read alignment was not done, which caused all the following errors.

Could you double check if you have minimap2 executable in your PATH? For example, if you run “minimap2 -h” in your terminal, could you see the manual of minimap2? If you could not print the minimap2 manual, you will need to install it and make sure to add the path to minimap2 to your $PATH.

Best, Maggi