search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
763 stars 138 forks source link

Issues with pathracer after 4.0 update #1401

Closed myco-bradshaw closed 3 weeks ago

myco-bradshaw commented 4 weeks ago

Description of bug

Hello,

Since the update to Spades 4.0, it seems that Pathracer no longer functions the way it did in the 3.16dev version. Since updating to the newest version, whenever I run patherracer in the same way as the previous version I get numerous errors with parsing as well as a fatal error .

error: while parsing GFA path record | 1 | P\tNODE_734_length_3605_cov_30.846463\t1201783+;1176853-\t* | ^ expected '\t'

Command: pathracer ~/HMM/path/file.hmm \ *assembly_graph_with_scaffolds.gfa -t 12 --parallel-components --memory 64 --output ./pathracer_genes/gene

Fatal error: Fatal exception (source file /__w/spades/spades/ext/src/hmmer/src/p7_pipeline.c, line 714): Target sequence length > 100K, over comparison pipeline limit. (Did you mean to use nhmmer/nhmmscan?)

spades.log

n/a

params.txt

n/a

SPAdes version

4.0

Operating System

Linux

Python Version

No response

Method of SPAdes installation

conda

No errors reported in spades.log

asl commented 4 weeks ago

@myco-bradshaw Will you please attach the example graph?

myco-bradshaw commented 4 weeks ago

assembly_graph_with_scaffolds.zip

Attached, I also noticed that patracher no longer seems to work with assemblies generated from older (3.15) spades builds.

asl commented 2 weeks ago

The fix should be available as a part of continuous build : https://github.com/ablab/spades/releases/tag/continuous