alekseyzimin
commented
4 years ago Hi, Thank you for pointing this out --this is a bug in specifying paths to files. Just fixed it, in the new 3.3.9 version. Please download and install the updated version from the releases. Best, Aleksey
I have assembled a bacterial genome from Nanopore long reads using Flye and would like to use polca to polish them using the Illumina paired short reads. I have installed Masurca by cloning from github and used the install.sh script on version MaSuRCA-3.3.8b. I have then skipped straight to the bottom to run polca but am getting a file can't open error message which doesn't make sense to me as polca seems to have already opened the file to index it.
The error is: ~/masurca/MaSuRCA-3.3.8b/bin/polca.sh -a /media/batdata/hybrid/comoros_bat/flye/17_5_F37_1/assembly.fasta -r '/media/batdata/hybrid/comoros_bat/27202_175F371_1_trimmed.fastq.gz /media/batdata/hybrid/comoros_bat/27202_175F371_2_trimmed.fastq.gz' /home/ubuntu/miniconda3/envs/bwa/bin/bwa /home/ubuntu/masurca/MaSuRCA-3.3.8b/bin/freebayes /home/ubuntu/masurca/MaSuRCA-3.3.8b/bin/samtools [Mon Feb 24 16:29:21 UTC 2020] Creating BWA index for /media/batdata/hybrid/comoros_bat/flye/17_5_F37_1/assembly.fasta [Mon Feb 24 16:29:24 UTC 2020] Aligning reads to /media/batdata/hybrid/comoros_bat/flye/17_5_F37_1/assembly.fasta [Mon Feb 24 16:30:29 UTC 2020] Sorting and indexing alignment file [samopen] SAM header is present: 4 sequences. [Mon Feb 24 16:30:59 UTC 2020] Calling variants in assembly.fasta Processing 2 scaffold(s) per batch could not open ..//media/batdata/hybrid/comoros_bat/flye/17_5_F37_1/assembly.fastacould not open ..//media/batdata/hybrid/comoros_bat/flye/17_5_F37_1/assembly.fasta
[Mon Feb 24 16:30:59 UTC 2020] Variant calling failed on batch 1 in assembly.fasta.work [Mon Feb 24 16:30:59 UTC 2020] Variant calling failed in ./assembly.fasta.work
Any ideas?