search

alekseyzimin / masurca

GNU General Public License v3.0
239 stars 35 forks source link

Error in masurca-polish tool #133

Open kataksk opened 4 years ago

kataksk commented 4 years ago

I'm trying to polish my assembly genome using masurca-polish tools, but get the error below.

[Wed Oct 2 00:33:48 JST 2019] Creating BWA index for /PATH/TO/genome.fasta [Wed Oct 2 01:09:02 JST 2019] Aligning reads to /PATH/TO/genome.fasta [Wed Oct 2 07:11:35 JST 2019] Sorting and indexing alignment file [Wed Oct 2 14:33:36 JST 2019] Calling variants Processing 934 scaffold(s) per batch could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta could not open ..//PATH/TO/genome.fasta [Wed Oct 2 14:33:42 JST 2019] Variant calling failed on batch 1 in genome.fasta.work

BWA seems successfully to recognize the path to genome.fasta But it fails to recognize the path during variant calling. Does anyone know about how to fix it? Thank you very much in advance!!

malonge commented 4 years ago

Does it work if you link all of the files to your current working directory? Then, when executing, remove the paths before the files.