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I am facing the following error while running the code -
Command line: ./IsoQuant/isoquant.py --reference Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --genedb Homo_sapiens.GRCh38.111.gtf.gz --fastq ../data/Nalm6_EV_full_length_reads.fastq --labels Nalm6_EV --data_type nanopore --output Nalm6_EV_isoquant --threads 4 --count_exons --check_canonical --splice_correction_strategy default_ont --model_construction_strategy default_ont --report_novel_unspliced true --gene_quantification with_ambiguous --min_mapq 5
2024-05-05 11:19:09,368 - INFO - Running IsoQuant version 3.3.1
2024-05-05 11:19:09,378 - INFO - === IsoQuant pipeline started ===
2024-05-05 11:19:09,379 - INFO - Converting gene annotation file to .db format (takes a while)...
2024-05-05 18:36:49,345 - INFO - Gene database written to /mnt/bioadhoc/Groups/vd-ay/abhijit/overflow/proj_overflow/ONTData/isoform/sampleWiseRuns/Nalm6_EV_isoquant/Homo_sapiens.GRCh38.111.gtf.db
2024-05-05 18:36:49,345 - INFO - Provide this database next time to avoid excessive conversion
2024-05-05 18:36:49,512 - INFO - Indexing reference
2024-05-05 18:38:45,623 - CRITICAL - IsoQuant failed with the following error, please, submit this issue to https://github.com/ablab/IsoQuant/issuesTraceback (most recent call last):
File "/mnt/bioadhoc/Groups/vd-ay/abhijit/overflow/proj_overflow/ONTData/isoform/sampleWiseRuns/./IsoQuant/isoquant.py", line 772, in <module>
main(sys.argv[1:])
File "/mnt/bioadhoc/Groups/vd-ay/abhijit/overflow/proj_overflow/ONTData/isoform/sampleWiseRuns/./IsoQuant/isoquant.py", line 766, in main
run_pipeline(args)
File "/mnt/bioadhoc/Groups/vd-ay/abhijit/overflow/proj_overflow/ONTData/isoform/sampleWiseRuns/./IsoQuant/isoquant.py", line 712, in run_pipeline
args.input_data = dataset_mapper.map_reads(args)
File "/mnt/bioadhoc/Groups/vd-ay/abhijit/overflow/proj_overflow/ONTData/isoform/IsoQuant/src/read_mapper.py", line 51, in map_reads
annotation_file = find_annotation(self.aligner, args)
File "/mnt/bioadhoc/Groups/vd-ay/abhijit/overflow/proj_overflow/ONTData/isoform/IsoQuant/src/read_mapper.py", line 258, in find_annotation
bed_fname = find_stored_bed(args)
File "/mnt/bioadhoc/Groups/vd-ay/abhijit/overflow/proj_overflow/ONTData/isoform/IsoQuant/src/read_mapper.py", line 121, in find_stored_bed
converted_beds = json.load(f_in)
File "/mnt/hpc-apps/python/3.10.10/lib/python3.10/json/__init__.py", line 293, in load
return loads(fp.read(),
File "/mnt/hpc-apps/python/3.10.10/lib/python3.10/json/__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "/mnt/hpc-apps/python/3.10.10/lib/python3.10/json/decoder.py", line 340, in decode
raise JSONDecodeError("Extra data", s, end)
json.decoder.JSONDecodeError: Extra data: line 1 column 1784 (char 1783)
Your help will be greatly appreciated.
The text was updated successfully, but these errors were encountered:
This is quite odd, as JSON configs are created and loaded by the same library.
It may be possible that there is some discrepancies between different IsoQuant versions and old contigs become unreadable.
I'd suggest to remove .config/IsoQuant/ directory in you home folder and try running again.
P.S. To speed up next run, provide .db file you got during this run (/mnt/bioadhoc/Groups/vd-ay/abhijit/overflow/proj_overflow/ONTData/isoform/sampleWiseRuns/Nalm6_EV_isoquant/Homo_sapiens.GRCh38.111.gtf.db) via --genedb option.
Usually, IsoQuant finds it automatically using those JSON configs, but in this case all JSON configs will be removed.
Hi,
I am facing the following error while running the code -
Your help will be greatly appreciated.
The text was updated successfully, but these errors were encountered: