Closed yuntwang closed 5 years ago
What was the error exactly?
@bsipos I am sorry The error like this: polish_clusters: 15:43:24 Failed running command: samtools view -h - exit status 1 but the samtools exists: samtools
Program: samtools (Tools for alignments in the SAM format) Version: 0.1.18 (r982:295)
Usage: samtools
Command: view SAM<->BAM conversion sort sort alignment file mpileup multi-way pileup depth compute the depth faidx index/extract FASTA tview text alignment viewer index index alignment idxstats BAM index stats (r595 or later) fixmate fix mate information flagstat simple stats calmd recalculate MD/NM tags and '=' bases merge merge sorted alignments rmdup remove PCR duplicates reheader replace BAM header cat concatenate BAMs targetcut cut fosmid regions (for fosmid pool only) phase phase heterozygotes
It seems your samtools is very old. Could you please install the lates version from bioconda and try again.
Thanks
Hi, I use the polish_clusters to correct my nanopore data and hope to get the consensus fasta, and I encounter an error. My command line: /polish_clusters -a data.clusters.tsv -o data.consensus.fasta -t 10 -c 5 -d ./data/temp data.sorted.bam why? Hope to get your reply. Thanks