Bug#962292: Help needed: Bug#962292: ITP: flye -- de novo assembler for single molecule sequencing reads using repeat graphs
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 <tille@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-packaging@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
--
http://fam-tille.de
Reply to: