database disk image is malformed

[dawangran]

Hello, I encountered the following error when using isoquant tool. May I ask what the reason is and how to solve it?

Command line: /usr/local/envs/isoquant36/bin/isoquant.py --data_type nanopore --bam 04.dedup/pbmc_1_NB_sorted.duplicates.directional.bam --read_group tag:NB --complete_genedb --genedb /ldfssz4/tmpfs/ST_BI/workflow/prd/cromwell-executions-volcano/scRNACycloneAnalysis/d248cc82-5140-4c63-af9c-587244603240/call-Quant/inputs/-498723670/genes.gtf --reference /ldfssz4/tmpfs/ST_BI/workflow/prd/cromwell-executions-volcano/scRNACycloneAnalysis/d248cc82-5140-4c63-af9c-587244603240/call-Quant/inputs/-498723670/genome.fasta --output 05.quant --sqanti_output --count_exons --threads 64 --check_canonical --force --clean_start
2025-02-14 05:22:51,886 - INFO - Running IsoQuant version 3.6.1
2025-02-14 05:22:51,909 - INFO - Novel unspliced transcripts will not be reported, set --report_novel_unspliced true to discover them
2025-02-14 05:22:51,909 - INFO - === IsoQuant pipeline started ===
2025-02-14 05:22:51,909 - INFO - gffutils version: 0.13
2025-02-14 05:22:51,909 - INFO - pysam version: 0.22.1
2025-02-14 05:22:51,909 - INFO - pyfaidx version: 0.8.1.3
2025-02-14 05:22:51,909 - INFO - Checking input gene annotation
2025-02-14 05:23:59,748 - INFO - Gene annotation seems to be correct
2025-02-14 05:23:59,881 - INFO - Converting gene annotation file to .db format (takes a while)...
2025-02-14 05:32:48,165 - CRITICAL - IsoQuant failed with the following error, please, submit this issue to https://github.com/ablab/IsoQuant/issuesTraceback (most recent call last):
File "/usr/local/envs/isoquant36/bin/isoquant.py", line 819, in
main(sys.argv[1:])
File "/usr/local/envs/isoquant36/bin/isoquant.py", line 813, in main
run_pipeline(args)
File "/usr/local/envs/isoquant36/bin/isoquant.py", line 749, in run_pipeline
args.genedb = convert_gtf_to_db(args)
File "/usr/local/envs/isoquant36/share/isoquant-3.6.1-0/src/gtf2db.py", line 144, in convert_gtf_to_db
gtf_filename, genedb_filename = convert_db(gtf_filename, genedb_filename, gtf2db, args)
File "/usr/local/envs/isoquant36/share/isoquant-3.6.1-0/src/gtf2db.py", line 360, in convert_db
convert_fn(gtf_filename, genedb_filename, args.complete_genedb, args.gtf_check)
File "/usr/local/envs/isoquant36/share/isoquant-3.6.1-0/src/gtf2db.py", line 133, in gtf2db
gffutils.create_db(gtf, db, force=True, keep_order=True, merge_strategy='error',
File "/usr/local/envs/isoquant36/lib/python3.8/site-packages/gffutils/create.py", line 1401, in create_db
c.create()
File "/usr/local/envs/isoquant36/lib/python3.8/site-packages/gffutils/create.py", line 545, in create
self._finalize()
File "/usr/local/envs/isoquant36/lib/python3.8/site-packages/gffutils/create.py", line 517, in _finalize
c.execute("CREATE INDEX featuretype ON features (featuretype)")
sqlite3.DatabaseError: database disk image is malformed

Best

Dawn

[andrewprzh]

Dear Dawn

Is it possible that you are using some kind of network shared disk, e.g. NFS?
Gffutils need to store the database on a local disk. For that, you can use --genedb_output option (see https://ablab.github.io/IsoQuant/cmd.html)

Best
Andrey