The program was terminated by segmentation fault

[laribritto]

Description of bug

I was running Unicycler, and during the execution of SPADES, an error occurred, causing it to stop

spades.log

Command line: /data/home/larissa.brito/miniconda3/envs/uni/bin/spades.py -1 >

System information: SPAdes version: 3.13.1 Python version: 3.7.11 OS: Linux-5.10.0-23-amd64-x86_64-with-debian-11.6

Output dir: /storages/caico/home/larissa.brito/ciclideos/SRR21777680/unicycler/output> Mode: ONLY read error correction (without assembling) Debug mode is turned OFF

Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (si> Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/storages/caico/home/larissa.brito/ciclideos/SRR21777680/unicycle> right reads: ['/storages/caico/home/larissa.brito/ciclideos/SRR21777680/unicycl> interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Other parameters: Dir for temp files: /storages/caico/home/larissa.brito/ciclideos/SRR21777680/unicyc> Threads: 8 Memory limit (in Gb): 125

======= SPAdes pipeline started. Log can be found here: /storages/caico/home/larissa.>

===== Read error correction started.

== Running read error correction tool: /storages/caico/home/larissa.brito/miniconda3/>

The program was terminated by segmentation fault === Stack Trace ===

== Error == system call for: "['/storages/caico/home/larissa.brito/miniconda3/envs/u>

In case you have troubles running SPAdes, you can write to [email protected] or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory.

params.txt

Command line: /data/home/larissa.brito/miniconda3/envs/uni/bin/spades.py -1 >

System information: SPAdes version: 3.13.1 Python version: 3.7.11 OS: Linux-5.10.0-23-amd64-x86_64-with-debian-11.6

Output dir: /storages/caico/home/larissa.brito/ciclideos/SRR21777680/unicycler/output> Mode: ONLY read error correction (without assembling) Debug mode is turned OFF

Dataset parameters: Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (si> Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/storages/caico/home/larissa.brito/ciclideos/SRR21777680/unicycle> right reads: ['/storages/caico/home/larissa.brito/ciclideos/SRR21777680/unicycl> interlaced reads: not specified single reads: not specified merged reads: not specified Read error correction parameters: Iterations: 1 PHRED offset will be auto-detected Corrected reads will be compressed Other parameters: Dir for temp files: /storages/caico/home/larissa.brito/ciclideos/SRR21777680/unicyc> Threads: 8 Memory limit (in Gb): 125

SPAdes version

SPAdes v. 3.13.1

Operating System

Linux-5.10.0-23-amd64-x86_64-with-debian-11.6

Python Version

Python v. 3.7.11

Method of SPAdes installation

conda

No errors reported in spades.log

• [ ] Yes

[asl]

For some reason SPAdes crashed during the start. It might be related to some conda-connected incompatibility. But since we're not maintaining these packaged you'd better ask conda.