Using sqm_annot.pl, died at line 223

gracegyho commented 11 months ago

I am trying to annotate two faa files with sqm_annot.pl.

sample_file.txt is in this format

sample1    sample1.faa aa
sample2    sample2.faa   aa

Where sample1.faa and sample2.faa are in Dummy_Dir. They are in fasta format and are prodigal-predicted genes. They have * characters in the sequence, but I also tried removing them and I get the same result below (Died at line 223).

$ sqm_annot.pl -s sample_file.txt -f Dummy_Dir/ 

SQM_annot v1.6.3, September 2023 - (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.

***

SqueezeMeta v1.6.3, September 2023 - (c) J. Tamames, F. Puente-SÃ¡nchez 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 Tue Oct 24 15:00:37 2023 in sequential mode
2 metagenomes found: Day_20200326 AUR2020_reps

--- SAMPLE Day_20200326 ---
Now creating directories
Reading configuration from /bioinf/home/gho/Sorted_Proteomics/databases/Metagenome/Annotations/Day_20200326/SqueezeMeta_conf.pl
  Running trimmomatic (Bolger et al 2014, Bioinformatics 30(15):2114-20) for quality filtering
  Parameters: 
  Directory structure and conf files created. Exiting
Died at /home/gho/miniconda3/envs/SqueezeMeta/bin/sqm_annot.pl line 223, <in> line 2.

I tried checking the manual but I can't figure out what's wrong...

jtamames commented 11 months ago

Hello Please edit the sqm_annot.pl script, and comment line 113. Change: if($ecode!=0) { catch_error(); } to #if($ecode!=0) { catch_error(); }

It should work that way. Best, J

gracegyho commented 11 months ago

It worked! 🎉

Thanks!

jtamames / SqueezeMeta

Using sqm_annot.pl, died at line 223 #742