[BUG] Macaca fascicularis sqanti_qc.py error

[sfodel]

Is there an existing issue for this?

• I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Problem description

Following Pablo's recommendation to open an issue here, from the original question: #498

In short, my sqanti_qc.py fails for a Macaca fascicularis novel-generated transcriptome (coming from isoseq collapse - original output produced using PacBio kinnex):

conda run sqanti3_qc.py hq_transcripts_CynoH_uniques.fa Macaca_fascicularis.Macaca_fascicularis_6.0.114.chr.gtf Macaca_fascicularis.Macaca_fascicularis_6.0.dna_sm.toplevel.fa -o CynoH_SQANTI -t 60 --force_id_ignore --report skip

my hq_transcripts_CynoH_uniques.fa has all unique entries, formatted like:

transcript/2146606 sample:BioSample_2

That's why I use the --force_id_ignore parameter.

Any idea what might be causing this error?

Thank you in advance,
Stelios

Code sample

sudo docker run -it -u $(id -u):$(id -g) -v /home/Cyno/:/data2 sqanti3 sqanti3_qc.py hq_transcripts_CynoH_uniques.fa Macaca_fascicularis.Macaca_fascicularis_6.0.114.chr.gtf Macaca_fascicularis.Macaca_fascicularis_6.0.dna_sm.toplevel.fa -o CynoH_SQANTI -t 60 --force_id_ignore --report skip

Error

This is the traceback:

**** Predicting ORF sequences...
Running ORF prediction on /data2/CynoH_SQANTI_corrected.fasta
**** Parsing Reference Transcriptome....
./refAnnotation_CynoH_SQANTI.genePred already exists. Using it.
**** Parsing Isoforms....
No short-reads or coverage provided. Skipping short-read coverage calculation.
**** TSS ratio will not be calculated since SR information was not provided
**** Performing Classification of Isoforms....
Traceback (most recent call last):
File "/opt2/sqanti3/5.3.6/SQANTI3-5.3.6/sqanti3_qc.py", line 84, in
main()
File "/opt2/sqanti3/5.3.6/SQANTI3-5.3.6/sqanti3_qc.py", line 68, in main
run(args)
File "/opt2/sqanti3/5.3.6/SQANTI3-5.3.6/src/qc_pipeline.py", line 92, in run
isoforms_info, ratio_TSS_dict = isoform_classification_pipeline(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt2/sqanti3/5.3.6/SQANTI3-5.3.6/src/classification_main.py", line 62, in isoform_classification_pipeline
assign_genomic_coordinates(isoform_hit, rec)
File "/opt2/sqanti3/5.3.6/SQANTI3-5.3.6/src/classification_steps.py", line 99, in assign_genomic_coordinates
isoform_hit.CDS_genomic_start = m[isoform_hit.CDS_start-1] + 1 # make it 1-based
~^^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: 2482
ERROR conda.cli.main_run:execute(125): conda run sqanti3_qc.py hq_transcripts_CynoH_uniques.fa Macaca_fascicularis.Macaca_fascicularis_6.0.114.chr.gtf Macaca_fascicularis.Macaca_fascicularis_6.0.dna_sm.toplevel.fa -o CynoH_SQANTI -t 60 --force_id_ignore --report skip failed. (See above for error)

Anything else?

No response

[pabloati]

Hi Stelios, could you try to run SQANTI3 on its latest release? We currently have verison 5.5 on docker as well, and let me know if the issue is still there :)

Pablo