search

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
348 stars 81 forks source link

Error in Spades assembly (ver1.6.2 post3) #709

Closed RIJP-SU closed 10 months ago

RIJP-SU commented 1 year ago

Hi, I updated SqueezeMeta so that Spades assembly can work. The newest version of SqueezeMeata (v1.6.2post3) indeed started Spades assembly normally but finished abnormally. Running Spades alone in conda environment generated error so problem would be on Spades.

Even same version of Spades (3.15.5), running in native environment finished normmaly.

I am attaching spades.log both from conda environment (with error) and naitive environment (normmaly finished). One difference between conda and naitve environment is version of python, would it be a problem? Any solution would be appreciated.

(conda)spades.log

(native) spades.log

fpusan commented 1 year ago

It works in my system. What is your OS and version? It is possible that the SPAdes binaries are not working properly for you, as per https://github.com/ablab/spades/issues/1094

fpusan commented 1 year ago

Also how are you installing SPAdes in the "native environment" exactly? Are you compiling from source or using the pre-compiled binaries?

RIJP-SU commented 1 year ago

Thanks fpusan, My OS is Ubuntu 20.04LTS. As same as #1094, I've got "OS return value: -11". So is this OS dependent problem and is not able to solve so far?

I could proceed next step by manually add contig file to result directory. Is this ok?

I installed Spades by conda, "naitive environement" means "base" environment. Sorry for cofusion.

fpusan commented 1 year ago

Weird, I also have Ubuntu 20.04 LTS. What's the output of uname -a?

RIJP-SU commented 1 year ago

Sorry what does "uname -a" mean?

fpusan commented 1 year ago

Just run the command, will tell us your exact distro and kernel version. Instead of adding the contig file to the result directory, call SqueezeMeta like this SqueezeMeta.pl -m coassembly -p Hadza2 --extassembly spades_assembly.fasta -f /your/raw/dir -s your.samples -contigid spades

RIJP-SU commented 1 year ago

Thanks, output of uname -a is follows. Linux "username" 5.15.0-76-generic #83~20.04.1-Ubuntu SMP Wed Jun 21 20:23:31 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

Regarding SqueezeMeta.pl -m coassembly -p Hadza2 --extassembly spades_assembly.fasta -f /your/raw/dir -s your.samples -contigid spades

Is "spades_assembly.fasta" name of contig file generated by Spada?

fpusan commented 1 year ago

Is "spades_assembly.fasta" name of contig file generated by Spada?

Yes

RIJP-SU commented 1 year ago

I changed path to Spades in SqueezeMeta_conf.pl from "$installpath/bin/SPAdes/spades.py" to "/path/to/minoconda3/bin/spades.py" <-installed via conda to base environment

Then, it worked fine. Thanks.

fpusan commented 10 months ago

Glad to hear it works, that's a good workaround. I am trying to find a more permanent solution to some binaries (mainly SPAdes and metabat) not working for some distros/versions... hopefully I'll get this done by the next version. Closing issue, feel free to reopen if needed.