Control: tags -1 help Hi,
I made some progress with this package and I actually expected it to work but there seems to be some issue with a minimap2 call. So if you clone the repository, build and install the package please follow the docs/USAGE.md document for testing by wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta flye --pacbio-raw E.coli_PacBio_40x.fasta --out-dir out_pacbio --genome-size 5m --threads 4 For me it runs a couple of minutes but than it exits with an error which is logged here: tail out_pacbio/flye.log [2020-06-05 18:48:06] INFO: Generating sequence [2020-06-05 18:51:45] DEBUG: Writing FASTA [2020-06-05 18:51:45] DEBUG: Peak RAM usage: 2 Gb -----------End assembly log------------ [2020-06-05 18:51:45] root: DEBUG: Disjointigs length: 4888051, N50: 4850514 [2020-06-05 18:51:45] root: INFO: >>>STAGE: consensus [2020-06-05 18:51:45] root: INFO: Running Minimap2 [2020-06-05 18:51:45] root: ERROR: Error running minimap2, terminating. See the alignment error log for details: out_pacbio/10-consensus/minimap.stderr [2020-06-05 18:51:45] root: ERROR: Command '['/bin/bash', '-c', 'set -o pipefail; /usr/bin/minimap2 out_pacbio/10-consensus/chunks.fasta E.coli_PacBio_40x.fasta -x map-pb -t 4 -a -p 0.5 -N 10 --sam-hit-only -L -Q --secondary-seq | /usr/bin/samtools view -T out_pacbio/10-consensus/chunks.fasta -u - | /usr/bin/samtools sort -T out_pacbio/10-consensus/sort_200605_185145 -O bam -@ 4 -l 1 -m 1G']' returned non-zero exit status 1. [2020-06-05 18:51:45] root: ERROR: Pipeline aborted (explicit paths shortened) I tried the very command that is actually run: $ /usr/bin/minimap2 out_pacbio/10-consensus/chunks.fasta E.coli_PacBio_40x.fasta -x map-pb -t 4 -a -p 0.5 -N 10 --sam-hit-only -L -Q --secondary-seq [ERROR] unknown option in "E.coli_PacBio_40x.fasta" Exit code: 1 It seems to me as if the code is creating a broken minimap2 command and I wonder whether anybody could fix this. BTW, it would also help if we could find a shorter sequence example than the given one that could be used for an autopkgtest. For my taste its unnecessarily long. Thanks for any help Andreas. [1] https://salsa.debian.org/med-team/flye On Fri, Jun 05, 2020 at 07:39:20PM +0200, Andreas Tille wrote: > Package: wnpp > Severity: wishlist > > Subject: ITP: flye -- de novo assembler for single molecule sequencing reads > using repeat graphs > Package: wnpp > Owner: Andreas Tille <ti...@debian.org> > Severity: wishlist > > * Package name : flye > Version : 2.7.1 > Upstream Author : , The Regents of the University of California > * URL : https://github.com/fenderglass/Flye > * License : BSD-3-Clause > Programming Lang: C > Description : de novo assembler for single molecule sequencing reads > using repeat graphs > Flye is a de novo assembler for single molecule sequencing reads, such > as those produced by PacBio and Oxford Nanopore Technologies. It is > designed for a wide range of datasets, from small bacterial projects to > large mammalian-scale assemblies. The package represents a complete > pipeline: it takes raw PacBio / ONT reads as input and outputs polished > contigs. Flye also has a special mode for metagenome assembly. > > Remark: This package is maintained by Debian Med Packaging Team at > https://salsa.debian.org/med-team/flye > > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
