The error encountered when running metaplasmidspades.py

[ucaswhw]

Description of bug

Here is my command: metaplasmidspades.py --only-assembler -1 ../cleandata/P_Cu_2/P_Cu_2_R1.fq.gz -2 ../cleandata/P_Cu_2/P_Cu_2_R2.fq.gz --assembly-graph P_Cu_2/assembly_graph_with_scaffolds.gfa -k 55 -o P_Cu_2_plasmid_test -t 24 -m 1000
I used the assembly_graph_with_scaffolds.gfa output from MetaSPAdes without any modifications. Additionally, I tested both the precompiled and locally compiled versions of SPAdes 4.0.0, but the error still persists.

error1:
error: while parsing GFA path record
|
1 | P\tNODE_21572222_length_146_cov_7.527473\t512564113+;80180755+\t*
| ^ expected '\t'

error2:
Verification of expression 'false' failed in function 'size_t debruijn_graph::DeBruijnGraph::link_length(debruijn_graph::DeBruijnGraph::VertexId, debruijn_graph::DeBruijnGraph::EdgeId, debruijn_graph::DeBruijnGraph::EdgeId) const'. In file '/mnt/sdb/yemao/wuhaowei/SPAdes-4.0.0/src/common/assembly_graph/core/graph.hpp' on line 141. Message 'Link 11459731 -> 7758781 was not found for vertex 15517558'.
Verification of expression 'false' failed in function 'size_t debruijn_graph::DeBruijnGraph::link_length(debruijn_graph::DeBruijnGraph::VertexId, debruijn_graph::DeBruijnGraph::EdgeId, debruijn_graph::DeBruijnGraph::EdgeId) const'. In file '/mnt/sdb/yemao/wuhaowei/SPAdes-4.0.0/src/common/assembly_graph/core/graph.hpp' on line 141. Message 'Link 11459731 -> 7758781 was not found for vertex 15517558'.
spades-core: /mnt/sdb/yemao/wuhaowei/SPAdes-4.0.0/src/common/assembly_graph/core/graph.hpp:141: size_t debruijn_graph::DeBruijnGraph::link_length(debruijn_graph::DeBruijnGraph::VertexId, debruijn_graph::DeBruijnGraph::EdgeId, debruijn_graph::DeBruijnGraph::EdgeId) const: Assertion `false' failed.

== Error == system call for: "['/mnt/sdb/yemao/wuhaowei/SPAdes-4.0.0/bin/spades-core', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/config.info', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/mda_mode.info', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/meta_mode.info', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/plasmid_mode.info', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/metaplasmid_mode.info']" finished abnormally, OS return value: -6

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes 4.0.0

Operating System

Linux version 5.15.0-72-generic

Python Version

Python 3.8

Method of SPAdes installation

manual compiled

No errors reported in spades.log

• Yes

[asl]

Dup of #1342

This is known issue with SPAdes 4.0. It was fixed in #1405

Consider trying latest snapshot from https://github.com/ablab/spades/releases/tag/continuous

[ucaswhw]

I used the version from https://github.com/ablab/spades/releases/tag/continuous, but the error still occurs.

/mnt/sdb/yemao/wuhaowei/spades-continuous/bin/spades-core(+0x7904e) [0x5561eeb5704e]
Verification of expression 'false' failed in function 'size_t debruijn_graph::DeBruijnGraph::link_length(debruijn_graph::DeBruijnGraph::VertexId, debruijn_graph::DeBruijnGraph::EdgeId, debruijn_graph::DeBruijnGraph::EdgeId) const'. In file '/mnt/sdb/yemao/wuhaowei/spades-continuous/src/common/assembly_graph/core/graph.hpp' on line 141. Message 'Link 10035250 -> 508102 was not found for vertex 1016200'.
Verification of expression 'false' failed in function 'size_t debruijn_graph::DeBruijnGraph::link_length(debruijn_graph::DeBruijnGraph::VertexId, debruijn_graph::DeBruijnGraph::EdgeId, debruijn_graph::DeBruijnGraph::EdgeId) const'. In file '/mnt/sdb/yemao/wuhaowei/spades-continuous/src/common/assembly_graph/core/graph.hpp' on line 141. Message 'Link 10035250 -> 508102 was not found for vertex 1016200'.
spades-core: /mnt/sdb/yemao/wuhaowei/spades-continuous/src/common/assembly_graph/core/graph.hpp:141: size_t debruijn_graph::DeBruijnGraph::link_length(debruijn_graph::DeBruijnGraph::VertexId, debruijn_graph::DeBruijnGraph::EdgeId, debruijn_graph::DeBruijnGraph::EdgeId) const: Assertion `false' failed.

== Error == system call for: "['/mnt/sdb/yemao/wuhaowei/spades-continuous/bin/spades-core', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/config.info', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/mda_mode.info', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/meta_mode.info', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/plasmid_mode.info', '/mnt/sdb/yemao/wuhaowei/spades/P_Cu_2_plasmid_test/K55/configs/metaplasmid_mode.info']" finished abnormally, OS return value: -6
None
params.txt
spades.log

[ucaswhw]

Is it caused by SPAdes exceeds the filesystem limit on open files?

[asl]

Is it caused by SPAdes exceeds the filesystem limit on open files?

No. Will you please attach the graph so we can reproduce the issue?

[ucaswhw]

I'm very happy to provide you with the graph file. However, I need to download it from the server first and then upload it to GitHub, which may take some time. I will upload it as soon as possible. Is there anything else you need besides the graph file?

[asl]

Should be enough for now. I'll let you know if this will be required

[ucaswhw]

Since I have reached the Git LFS file transfer limit, I have uploaded my graph files to Google Drive. Here is the link to the files. If this method is not suitable for you, please let me know, and I will find an alternative way to upload them to GitHub. Thank you!

https://drive.google.com/file/d/1AIOVEpeJcK241ftbzpegYFeovGt4Gw7_/view?usp=share_link

[ucaswhw]

Hi, I seem to be encountering the same issue while testing MetaViralSPAdes. I was running it on a different dataset, and it appears to be stuck at the same poin
spades.log
t.
params.txt

[asl]

@ucaswhw The second dataset is much smaller and it would be easier for us to reproduce. Will you please upload the graph and input files?

[ucaswhw]

Certainly, I’m more than happy to provide the requested file. Attached is my graph file. However, due to GitHub’s upload limitations, I will be uploading the clean data to Google Drive shortly.

If you need any additional files, please don’t hesitate to reach out at any time!

Best regards,

assembly_graph_with_scaffolds.gfa.zip

[ucaswhw]

This is the link of cleandata in google drive. If you need anything, please let me know
https://drive.google.com/file/d/1-N4_tHkxYYse0-e1ahlpLINqQ2mLtsYP/view?usp=sharing, https://drive.google.com/file/d/1-y6RH0BctFzLjdOrJ7sBkO8kkRj4iTRx/view?usp=sharing