SQANTI3 QC step fails with inclusion of FL count

[Motoufiq]

Hello,

I am currently using SQANTI3 v5.5.1 and encountered an error when running sqanti3_qc.py with a multi-sample FL count file using the --fl_count option. The job fails with the following message (see below):

My script:

singularity run /projects/palucka-lab/toufim/Tools/sqanti3.sif \

sqanti3_qc.py \
 --isoforms "$FLAIR_GTF" \
 --refGTF "$REF_GTF" \
 --refFasta "$GENOME"\
 -o "$OUTNAME" -d "$OUTDIR"\
 -c "$SPLICE_JXN_DIR"\
 --SR_bam "$SORTED_BAM_DIR"\
 --CAGE_peak "$CAGE"\
 --polyA_peak "$POLYA_PEAK"\
 --fl_count "$FL_QUANTIFY"\
 --aligner_choice=minimap2\
 --report pdf -n 10 -t 5

A colleague in our institute was able to run with theSQANTI v5.5.2. Is this version specific error?

It appears that the added FL count columns are not included in FIELDS_CLASS, causing the CSV writer to throw an error. Could you please confirm if this issue has been addressed in v5.5.2 or v5.5.3 or provide guidance on the best workaround?

Logs:

[INFO:2025-11-19 13:41:47,301] **** Reading Full-length read abundance files.
[INFO:2025-11-19 13:41:47,749] Multi-sample PacBio FL count format detected.
[WARNING:2025-11-19 13:41:47,751] Isoform transcript/835315 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,755] Isoform transcript/441121 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,768] Isoform transcript/6161191 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,769] Isoform transcript/2089755 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,771] Isoform transcript/94576 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,772] Isoform transcript/345279 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,775] Isoform transcript/482170 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,779] Isoform transcript/1901156 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,780] Isoform transcript/1209121 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,781] Isoform transcript/4690331 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,787] Isoform transcript/1334434 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,788] Isoform transcript/224830 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,792] Isoform transcript/3217521 not found in FL count file. Assign count as 0.
[WARNING:2025-11-19 13:41:47,794] Isoform transcript/2610760 not found in FL count file. Assign count as 0.
Traceback (most recent call last):
  File "/opt2/sqanti3/5.5.1/SQANTI3-5.5.1/sqanti3_qc.py", line 52, in <module>
    main()
  File "/opt2/sqanti3/5.5.1/SQANTI3-5.5.1/sqanti3_qc.py", line 41, in main
    combine_split_runs(args,split_dirs)
  File "/opt2/sqanti3/5.5.1/SQANTI3-5.5.1/src/parallel.py", line 198, in combine_split_runs
    write_classification_output(isoforms_info, outputClassPath, FIELDS_CLASS)
  File "/opt2/sqanti3/5.5.1/SQANTI3-5.5.1/src/qc_output.py", line 41, in write_classification_output
    fout_class.writerow(isoforms_info[iso_key].as_dict())
  File "/conda/miniconda3/envs/sqanti3/lib/python3.11/csv.py", line 154, in writerow
    return self.writer.writerow(self._dict_to_list(rowdict))
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/conda/miniconda3/envs/sqanti3/lib/python3.11/csv.py", line 149, in _dict_to_list
    raise ValueError("dict contains fields not in fieldnames: "
ValueError: dict contains fields not in fieldnames: 'FL.DD46_old_batch2', 'FL.DD140_old_batch2', 'FL.DD21_old_batch2', 'FL.DD48_young_batch2', 'FL.DD39_young_batch2', 'FL.DD51_young_batch2', 'FL.DD98_old_batch2', 'FL.DD83_old_batch2', 'FL.DD17_young_batch2', 'FL.DD58_young_batch2'
ERROR conda.cli.main_run:execute(127): `conda run sqanti3_qc.py --isoforms /projects/palucka-lab/RNAseq/

EPILOG
--
Job ID: 8890329
Cluster: sumner2
User/Group: toufim/jaxuser
State: FAILED (exit code 1)

Best Regards,
Toufiq

[pabloati]

This has been solved in issue #556