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nanoporetech / pinfish

Tools to annotate genomes using long read transcriptomics data
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error from polish_clusters #8

Closed yuntwang closed 5 years ago

yuntwang commented 5 years ago

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

bsipos commented 5 years ago

What was the error exactly?

yuntwang commented 5 years ago

@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 [options]

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

bsipos commented 5 years ago

It seems your samtools is very old. Could you please install the lates version from bioconda and try again.

yuntwang commented 5 years ago

Thanks