Assertion `path.Size() > 1' failed.

[437364]

Description of bug

Hello,

I'm running a Nanopore + Illumina hybrid assembly and I seem to be getting similar error some people have encountered with v3.12 (#43 ) even though I use newer version (v3.15.2).

spades-core: /scratch/vorel/SPAdes-3.15.2/src/common/modules/path_extend/path_extender.hpp:205: virtual size_t path_extend::PairedInfoLoopEstimator::EstimateSimpleCycleCount(const path_extend::BidirectionalPath&, path_extend::EdgeId, path_extend::EdgeId) const: Assertion `path.Size() > 1' failed.


== Error ==  system call for: "['/afs/ics.muni.cz/software/spades/3.15.2/bin/spades-core', '/scratch.ssd/kratka/job_10857670.meta-pbs.metacentrum.cz/spades/K127/configs/config.info']" finished abnormally, OS return value: -6

======= SPAdes pipeline finished abnormally and WITH WARNINGS!

=== Error correction and assembling warnings:
 * 0:43:29.444    14G / 25G   WARN    General                 (kmer_coverage_model.cpp   : 366)   Failed to determine erroneous kmer threshold. Threshold set to: 17
 * 0:38:46.981    13G / 26G   WARN    General                 (kmer_coverage_model.cpp   : 366)   Failed to determine erroneous kmer threshold. Threshold set to: 14
 * 0:37:29.661    14G / 28G   WARN    General                 (kmer_coverage_model.cpp   : 327)   Valley value was estimated improperly, reset to 5
 * 0:37:29.693    14G / 28G   WARN    General                 (kmer_coverage_model.cpp   : 366)   Failed to determine erroneous kmer threshold. Threshold set to: 5
 * 0:35:17.749    12G / 27G   WARN    General                 (kmer_coverage_model.cpp   : 327)   Valley value was estimated improperly, reset to 1
 * 0:30:12.493    12G / 25G   WARN    General                 (kmer_coverage_model.cpp   : 218)   Too many erroneous kmers, the estimates might be unreliable
 * 0:30:20.499    12G / 25G   WARN    General                 (kmer_coverage_model.cpp   : 366)   Failed to determine erroneous kmer threshold. Threshold set to: 136
 * 1:11:35.382    19G / 34G   WARN    General                 (simplification.cpp        : 500)   The determined erroneous connection coverage threshold may be determined improperly
 * 0:22:15.153    11G / 20G   WARN    General                 (kmer_coverage_model.cpp   : 366)   Failed to determine erroneous kmer threshold. Threshold set to: 163
 * 9:06:26.726    26G / 52G   WARN   ScaffoldingUniqueEdgeAna (scaff_supplementary.cpp   :  72)   Less than half of genome in unique edges!
======= Warnings saved to /scratch.ssd/kratka/job_10857670.meta-pbs.metacentrum.cz/spades/warnings.log

=== ERRORs:
 * system call for: "['/afs/ics.muni.cz/software/spades/3.15.2/bin/spades-core', '/scratch.ssd/kratka/job_10857670.meta-pbs.metacentrum.cz/spades/K127/configs/config.info']" finished abnormally, OS return value: -6

Please see the log and params files attached. Many thanks for your help!

spades.log

spades.log

params.txt

params.txt

SPAdes version

v3.15.2

Operating System

Debian 11

Python Version

Python 2.7.18

Method of SPAdes installation

No idea - module at computing cluster

No errors reported in spades.log

• [X] Yes

[asl]

We believe that this issue was fixed in SPAdes 3.15.3. Will you please give the latest released SPAdes (3.15.4) a try?

[437364]

We believe that this issue was fixed in SPAdes 3.15.3. Will you please give the latest released SPAdes (3.15.4) a try?

Unfortunately, I get the same error with 3.15.4.

params.txt spades.log

[asl]

Will it be possible to share your data with us, so we can reproduce an issue?

[437364]

I might have found the issue. I'm using two PE Illumina libraries with different read lengths (~150 and 250 bp). With the default k-mer sizes were 21, 33, 55, 77, 99, 127 it crashed. When I used only the shorter k-mers (max. 77), it didn't crash. Interestingly, a different dataset (with same library sizes) didn't crash even when used with the long k-mers.

[asl]

Well, still we need input data in order to reproduce an issue

[437364]

I discussed this with colleagues and unfortunately they are a bit averse to sharing our data. I'll let you know if the situation changes.