Exit with exception in 3.15.3 is now OS return value: -11 in 3.15.4

[samwichse]

Description of bug

I'm trying to assemble some data with an HMM and the --corona switch, but it was erroring out in 3.15.3 with an exception. So I updated SPAdes to 3.15.4 and running the same command now gives me an OS return value -11

The 3.15.4 error is particularly confusing:

== Error == system call for: "['/usr/local/bin/spades-core', '/mnt/Storage_Array/Shared/Sam/PasteBin/UWisc/SPAdes_20106-2/K73/configs/config.info', '/mnt/Storage_Array/Shared/Sam/PasteBin/UWisc/SPAdes_20106-2/K73/configs/mda_mode.info', '/mnt/Storage_Array/Shared/Sam/PasteBin/UWisc/SPAdes_20106-2/K73/configs/meta_mode.info', '/mnt/Storage_Array/Shared/Sam/PasteBin/UWisc/SPAdes_20106-2/K73/configs/rnaviral_mode.info', '/mnt/Storage_Array/Shared/Sam/PasteBin/UWisc/SPAdes_20106-2/K73/configs/hmm_mode.info']" finished abnormally, OS return value: -11.

Both logs and params are included, but I assume only 3.15.4 will be of interest?

spades.log

spades_3.15.3.log spades_3.15.4.log

params.txt

params_3.15.3.txt params_3.15.4.txt

SPAdes version

3.15.3 and 3.15.4

Operating System

Centos 7.9 3.10.0-1160.62.1.el7.x86_64 #1 SMP

Python Version

2.7.5

Method of SPAdes installation

binaries

No errors reported in spades.log

• [X] Yes

[asl]

What are the HMMs you're using?

[samwichse]

Just one built on an virus alignment with hmmbuild

HMMER3/f [3.1b2 | February 2015] NAME viral_alignment LENG 7941 MAXL 9826 ALPH DNA RF no MM no CONS yes CS no MAP yes DATE Thu Jun 23 14:18:40 2022 NSEQ 4 EFFN 3.144531

[asl]

I believe you need to use AA HMM

[samwichse]

OMG forehead smack

Unless they want to make it more idiot proof WRT errors, I'll close this, then.

[asl]

Yes, we will add checks in the next release.

[asl]

SPAdes 3.15.5 will have support for DNA HMMs

[samwichse]

Thanks, that would be very helpful!

[asl]

Fixed in https://github.com/ablab/spades/releases/tag/v3.15.5