Sqanti rescue fails without logs

[ludzkia]

Hello,

I submitted the following code to run Sqanti rescue in full mode, but the job completes with "completed" status in my job scheduler in just seconds:

#Define paths

FILTER_CLASS="/SQANTI3_filter/output_LRD_rules/isoforms_RulesFilter_result_classification.txt"
REFERENCE_ANNOTATION="/SQANTI3_QC/gencode/gencode.v47.chr_patch_hapl_scaff.annotation.gtf"
REFERENCE_GENOME="/SQANTI3_QC/gencode/GRCh38.p14.genome.fa"
LONG_READ_ISOFORMS=/SQANTI3_QC/output_LRD/isoforms_corrected.fasta
LONG_READ_FILTERED="/SQANTI3_filter/output_LRD_rules/isoforms.filtered.gtf"
CLASS_FILE="/QC_ref/isoforms_classification.txt"
FL_COUNT="/SQANTI3_QC/input_files/unfiltered_transcript_counts_superPBID.tsv"
OUTPUT_DIR="/Rescue/"
JSON_RULES_FILTER="~/SQANTI3_filter/filter_rules.json"

Run SQANTI3 QC

python sqanti3_rescue.py rules --filter_class "$FILTER_CLASS" --refGTF "$REFERENCE_ANNOTATION" --refFasta "$REFERENCE_GENOME" --rescue_isoforms "$LONG_READ_ISOFORMS" --rescue_gtf "$LONG_READ_FILTERED" --refClassif "$CLASS_FILE" --requant --counts "$FL_COUNT" --mode full -d "$OUTPUT_DIR" --cpus 24 -j "$JSON_RULES_FILTER" -v

It leaves only the following in the output log, despite verbose mode:
Starting SQANTI3 job on esplhpc-cp059 at Thu Jun 12 17:09:01 PDT 2025
SQANTI3 f5.4

The error log only has the Sqanti Rescue art.
I ran almost the same code in automatic mode and got expected output files. Not sure what could be wrong! We might have to keep digging into local issues and files but I thought to check with the community. Thanks!

[pabloati]

Hi, in SQANTI3 the -v option stands for --version, not for --verbose. It will override any other options you add, thus why you only see the art. Also, you might want to update your SQANTI to the latest release, 5.5 :)