issuesTraceback (most recent call last): File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 808, in <module> main(sys.argv[1:])

[JhinJhinJhin]

i check all of requirements.txt, so what's wrong?
isoquant.py --test
commond line: ~/mambaforge/envs/isoquant/bin/isoquant.py --test
=== Running in test mode ===
Any other option is ignored
2024-08-02 21:01:57,137 - INFO - Running IsoQuant version 3.4.2
2024-08-02 21:01:57,265 - INFO - Novel unspliced transcripts will not be reported, set --report_novel_unspliced true to discover them
2024-08-02 21:01:57,265 - INFO - === IsoQuant pipeline started ===
2024-08-02 21:01:57,265 - INFO - gffutils version: 0.13
2024-08-02 21:01:57,265 - INFO - pysam version: 0.22.1
2024-08-02 21:01:57,266 - INFO - pyfaidx version: 0.8.1.1
2024-08-02 21:01:57,286 - INFO - Checking input gene annotation
2024-08-02 21:01:57,305 - INFO - Gene annotation seems to be correct
2024-08-02 21:01:57,305 - INFO - Converting gene annotation file to .db format (takes a while)...
2024-08-02 21:01:57,331 - CRITICAL - IsoQuant failed with the following error, please, submit this issue to https://github.com/ablab/IsoQuant/issuesTraceback (most recent call last):
File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 808, in
main(sys.argv[1:])
File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 797, in main
args, parser = parse_args(args)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 254, in parse_args
args = parser.parse_args(cmd_args, namespace)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/argparse.py", line 1768, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/argparse.py", line 1800, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/argparse.py", line 2006, in _parse_known_args
start_index = consume_optional(start_index)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/argparse.py", line 1946, in consume_optional
take_action(action, args, option_string)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/argparse.py", line 1874, in take_action
action(self, namespace, argument_values, option_string)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 779, in call
main(options)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 802, in main
run_pipeline(args)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/bin/isoquant.py", line 741, in run_pipeline
args.genedb = convert_gtf_to_db(args)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/share/isoquant-3.4.2-0/src/gtf2db.py", line 145, in convert_gtf_to_db
gtf_filename, genedb_filename = convert_db(gtf_filename, genedb_filename, gtf2db, args)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/share/isoquant-3.4.2-0/src/gtf2db.py", line 303, in convert_db
convert_fn(gtf_filename, genedb_filename, args.complete_genedb, args.gtf_check)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/share/isoquant-3.4.2-0/src/gtf2db.py", line 130, in gtf2db
gffutils.create_db(gtf, db, force=True, keep_order=True, merge_strategy='error',
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/site-packages/gffutils/create.py", line 1401, in create_db
c.create()
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/site-packages/gffutils/create.py", line 542, in create
self._init_tables()
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/site-packages/gffutils/create.py", line 466, in _init_tables
self.set_pragmas(self.pragmas)
File "/lustre/home/jianghao/mambaforge/envs/isoquant/lib/python3.8/site-packages/gffutils/create.py", line 457, in set_pragmas
c.executescript(";\n".join(["PRAGMA %s=%s" % i for i in self.pragmas.items()]))
sqlite3.OperationalError: disk I/O error

[andrewprzh]

This looks like a disk I/O problem.
Is there a chance your run IsoQuant on some network disk, e.g. NFS share?

Best
Andrey

[JhinJhinJhin]

This looks like a disk I/O problem. Is there a chance your run IsoQuant on some network disk, e.g. NFS share?

Best Andrey

thank you!
i don't know why, Maybe it was caused by lustre?
Best wish for you.
Jhin

[andrewprzh]

I guess it can. IsoQuant uses gffutils, which creates and SQL database from the gene annotation on disk. Unfortunately, it is not possible to create a database connection on network disks.

Thus, I suggest to run test in some other location, i.e. local storage. If you need to run IsoQuant using lustre, you may use --genedb_output <local folder> option. This will create a database in a local folder, but the rest of the output will be in main output folder.

Best
Andrey

[JhinJhinJhin]

I guess it can. IsoQuant uses gffutils, which creates and SQL database from the gene annotation on disk. Unfortunately, it is not possible to create a database connection on network disks.

Thus, I suggest to run test in some other location, i.e. local storage. If you need to run IsoQuant using lustre, you may use --genedb_output <local folder> option. This will create a database in a local folder, but the rest of the output will be in main output folder.

Best Andrey

I understand, it can be used after I specify the dir in the /tmp directory. Thank you very much!!!

[JhinJhinJhin]

I guess it can. IsoQuant uses gffutils, which creates and SQL database from the gene annotation on disk. Unfortunately, it is not possible to create a database connection on network disks.

Thus, I suggest to run test in some other location, i.e. local storage. If you need to run IsoQuant using lustre, you may use --genedb_output <local folder> option. This will create a database in a local folder, but the rest of the output will be in main output folder.

Best Andrey

I'm getting this error again and using --genedb_output <local folder>option doesn't help. Can I provide the .db file input converted with gfftuils? How to do that? I only saw the sentence You can also provide gffutils database manually , but I don’t know how to do it.

[andrewprzh]

@JhinJhinJhin

You can provide the database using the same --genedb option.

Best
Andrey

[andrewprzh]

Also, IsoQuant contains a script for GTF <-> database conversion: src/gtf2db.py