04.rundiamond.pl error while using sqm_annot.pl

[PuspenduSardar]

Hello!

I am using sqm_annot.pl (modified as per your suggestion in the clossed-issue #540) to annotate a file with ~40 million predicted ORFs. The script repeatedly crashed, saying error running at line 72 of 04.rundiamond.pl and died at line 223 of sqm_annot.pl. I am using SqueezeMeta v1.5.2.

I am not sure what is wrong here! Is it a memory/space issue? I am running on 3 TB of free space with 480 GB memory and 86 threads.

Could you please help me with this?

Regards, Puspendu

[jtamames]

Hello Try updating to 1.6, several bugs were fixed for that script. Best, J

[PuspenduSardar]

Thanks, @jtamames. Do I still need to edit the sqm_annot.pl script to define the desired parameters? I have SqueezeMeta databases built, is v1.6 compatible with those databases?

Regards, Puspendu

[jtamames]

Hello Yes it is, no need to update the databases. Just use configure_nodb.pl.

[PuspenduSardar]

Hello Try updating to 1.6, several bugs were fixed for that script. Best, J

Hello @jtamames,

I installed the v1.6 and tried it. Now it's throwing up a new type of error (bug) which I never had from the previous version.

sqm_annot.pl -f . -s sample.file -t 86 --nocog

SQM_annot v1.6.0, September 2022 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

This is part of the SqueezeMeta distribution (https://github.com/jtamames/SqueezeMeta)
Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 10.3389 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

Now I will call SqueezeMeta to do my stuff. Please hold on.

mkdir: cannot create directory ‘/home/ps897/sharing/melanoma/contigs/fun_annot’: File exists

SqueezeMeta v1.6.0, September 2022 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

Please cite: Tamames & Puente-Sanchez, Frontiers in Microbiology 9, 3349 (2019). doi: https://doi.org/10.3389/fmicb.2018.03349

Run started Mon Oct 10 17:23:07 2022 in sequential mode
1 metagenomes found: sqm_out

--- SAMPLE sqm_out --------
Now creating directories
Reading configuration from /home/ps897/sharing/melanoma/contigs/fun_annot/sqm_out/SqueezeMeta_conf.pl
  Directory structure and conf files created. Exiting
Died at /home/ps897/miniconda3/envs/SqueezeMeta_1.6/bin/sqm_annot.pl line 223, <in> line 1.

Here is how my sample.file looks sqm_out melanoma_nr_prot_clean.faa aa

In fact, the script creates a directory named sqm_out but then stops.

Could you please let me know how to solve this?

Regards, Puspendu

[jtamames]

What is there in the sqm_out/results directory?

[PuspenduSardar]

Hello, Thanks. The sqm_out/results directory is empty! I have attached the screenshot of the sqm_out directory and SqueezeMeta_conf.pl and syslog (as .txt format). Many Thanks.

Regards, Puspendu

SqueezeMeta_conf.txt syslog.txt

[jtamames]

Where is your aa file stored? Is it in /home/ps897/sharing/melanoma/contigs/fun_annot? If so, what happens if you try to run the script with: sqm_annot.pl -f /home/ps897/sharing/melanoma/contigs/fun_annot -s sample.file -t 86 --nocog

[PuspenduSardar]

Tried! No luck. Same error. mkdir: cannot create directory ‘/home/ps897/sharing/melanoma/contigs/fun_annot’: File exists