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Hello,
i have a problem regarding polishing an assembly (created with Canu) using pair-end short reads.
The process seems to be stuck at the aligning reads step and the files created bwa.err are empty as well as the unsorted output. I get following output and i am running the latest docker image.
I hope someone can help me solving this isssue.
Thank you!
root@7ccf2665231b:/data/polishing_results# /usr/bin/time -v polca.sh -a Kpneumoniae.fasta -r '1KP_Illumina_SRR8482586.fastq 2KP_Illumina_SRR8482586.fastq'
/bwa/bwa-0.7.17/bwa
/MaSuRCA-4.1.0/bin/freebayes
/MaSuRCA-4.1.0/bin/samtools
[Fri Mar 31 17:19:26 UTC 2023] Aligning reads to Kpneumoniae.fasta
The text was updated successfully, but these errors were encountered:
Hello,
i have a problem regarding polishing an assembly (created with Canu) using pair-end short reads.
The process seems to be stuck at the aligning reads step and the files created bwa.err are empty as well as the unsorted output. I get following output and i am running the latest docker image.
I hope someone can help me solving this isssue.
Thank you!
root@7ccf2665231b:/data/polishing_results# /usr/bin/time -v polca.sh -a Kpneumoniae.fasta -r '1KP_Illumina_SRR8482586.fastq 2KP_Illumina_SRR8482586.fastq'
/bwa/bwa-0.7.17/bwa
/MaSuRCA-4.1.0/bin/freebayes
/MaSuRCA-4.1.0/bin/samtools
[Fri Mar 31 17:19:26 UTC 2023] Aligning reads to Kpneumoniae.fasta
The text was updated successfully, but these errors were encountered: