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aaranyue / quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification
http://atcgn.com:8080/quarTeT/home.html
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[ERROR] failed to open file 'quarTeT.flank_map_ILhap1hap2.fa.paf' #40

Open lijphd168866 opened 2 months ago

lijphd168866 commented 2 months ago

Hello, I used the GapFiller moduel of this tool and my command is as follows： python3 ~/biosoft/quarTeT/quartet.py GapFiller \ -d $draftgenome -g $hap1hap2.fa -t 32

and then,error follows:

[Info] Getting gaps flanking sequence... [Info] gapfilling with hap1hap2.fa... [Info] Running minimap2... [Error] Unexcepted error occur in minimap2 as follow: cmd: minimap2 -x asm5 -t 32 -c -o quarTeT.flank_map_hap1hap2.fa.paf ~./hap1hap2.fa tmp/quarTeT.gap.flanking.fasta returncode: 1 stdout:

stderr: [ERROR] failed to open file 'quarTeT.flank_map_hap1hap2.fa.paf' Thank you for the answers. best wishe

Echoring commented 2 months ago

This is a minimap2 error, likes like it cannot create a output file. There's 2 possibility:

  1. in this report, ~./hap1hap2.fa is set as reference genome, but looks not like a valid path. Check your varible $draftgenome and $hap1hap2.fa whether set to a valid path.
  2. You may not have write permission at current dir so minimap2 cannot create output file here?
lijphd168866 commented 2 months ago

Thanks for you answer, I checked my path and looked at the permissions without problems;I reinstalled minimap2 with conda，and then, I used the result of hifiasm assembled hifiasm.asm.hic.p_ctg.fa as a GAPCLOSER_CONTIG and output the same error

Echoring commented 2 months ago

This error is reported by called minimap2, not quarTeT. The failed command is listed in the error report start with cmd:. You can try to run this command directly and find what's wrong with minimap2.

DexinBo commented 2 months ago

Thanks for you answer, I checked my path and looked at the permissions without problems;I reinstalled minimap2 with conda，and then, I used the result of hifiasm assembled hifiasm.asm.hic.p_ctg.fa as a GAPCLOSER_CONTIG and output the same error

Hello, I encountered the same problem and later discovered that it may be caused by the Conda version of Minimap2=2.21, after switching to the compiled version of minimap2=2.28, this issue was resolved.