Stopping TAXONOMIC ASSIGNMENT: 06.lca.pl

[Mandeepumra]

SqueezeMeta v1.7.2, June 2025 - (c) J. Tamames, F. Puente-Sánchez CNB-CSIC, Madrid, SPAIN

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

Run started Tue Feb 24 11:11:52 2026 in extassembly mode
1 metagenomes found: IR2

Contig file /path/SqueezeMeta/scripts/IR2_project_new/results/01.IR2_project_new.fasta already found, skipping step 1
RNA gff file /path/IR2_project_new/intermediate/02.IR2_project_new.maskedrna.fasta already found, skipping step 2
Aminoacid file /path/IR2_project_new/results/03.IR2_project_new.faa already found, skipping step 3
Diamond file /path/IR2_project_new/intermediate/04.IR2_project_new.nr.diamond already found, skipping step 4
Pfam file /path/IR2_project_new/intermediate/05.IR2_project_new.pfam.hmm already found, skipping step 5
[0 seconds]: STEP6 -> TAXONOMIC ASSIGNMENT: 06.lca.pl
Stopping in STEP6 -> 06.lca.pl. File /path/IR2_project_new/results/06.IR2_project_new.fun3.tax.wranks is empty!

I have tried so many times but I am not able to sort it out.
help me out of this.
Thanks

[fpusan]

Can you share the /path/SqueezeMeta/scripts/IR2_project_new/syslog file?

Also, what's the output of head /path/IR2_project_new/intermediate/04.IR2_project_new.nr.diamond?

[Mandeepumra]

thank you fpusan for reply.

syslog_of_IR2_project_new.txt
head intermediate/04.IR2_project_new.nr.diamond
IR2_project_new_2_149-307 HYZ51466.1 95.3 43 2 0 11 53 1 43 2.55e-16 79.7
IR2_project_new_2_149-307 HJT50043.1 81.4 43 8 0 11 53 1 43 1.70e-13 72.4
IR2_project_new_2_149-307 HYY66639.1 69.8 43 13 0 11 53 1 43 2.29e-10 63.9
IR2_project_new_2_149-307 MDW3643273.1 65.1 43 15 0 11 53 1 43 8.25e-10 59.3
IR2_project_new_2_149-307 MDP9306603.1 69.8 43 13 0 11 53 1 43 2.34e-09 61.2
IR2_project_new_2_149-307 MDW0136708.1 67.4 43 14 0 11 53 1 43 2.37e-09 58.2
IR2_project_new_2_149-307 HXV89380.1 69.8 43 13 0 11 53 1 43 2.47e-09 61.2
IR2_project_new_2_149-307 HEU5446868.1 69.8 43 13 0 11 53 1 43 2.47e-09 61.2
IR2_project_new_2_149-307 HMG39354.1 69.8 43 13 0 11 53 1 43 2.50e-09 61.2
IR2_project_new_2_149-307 HEX5574180.1 69.8 43 13 0 11 53 1 43 2.64e-09 61.2

I have attached what you asked.
please let me know if you need anything else at my end.
thanks
-Mandeep

[fpusan]

Ok, so the contigs seem to be annotated.
Any chance you can share the whole /path/IR2_project_new/ project directory with me? perhaps through WeTransfer, Dropbox, MEGA, OneDrive etc...

[Mandeepumra]

https://drive.google.com/file/d/1W1wIpALtq-cGg34RA9zxiar6MIL7jMr8/view?usp=drive_link

As this is only one sample. I have to work on many more. If it sorted out please let me know.
--Thanks

[fpusan]

Got the data and I'm trying to reproduce the error, will let you know how it goes

[fpusan]

Ok, step 6 finished successfully for your data in my workstation so it's not a problem with your data or with our code (at least not an obvious bug).
We've seen issues like these when working on clusters and using a high number of processors.
Maybe you can:

1. edit the $numthreads variable in the /lustre/home/gylab204/BEEJ_Storage/software/SqueezeMeta/scripts/IR2_project_new/SqueezeMeta_conf.pl file, and set it to a smaller number of processors (maybe one).
2. launch a job with the command 06.lca.pl /lustre/home/gylab204/BEEJ_Storage/software/SqueezeMeta/scripts/IR2_project_new/. This will only run step 6, but only with one processor.
3. you can then edit the $threads variable and set it to a higher number, and restart the project from there after step 6 finishes successfully

[Mandeepumra]

I tried this but 06.lca.pl but its not running.

[fpusan]

That's strange, we'll keep our heads up and see if we can reproduce in a cluster. For now, I am attaching the result of running step 6 for that project, just put the files inside your own results folder and the pipeline should be able to resume from step 7.
test.zip