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SorenKarst / longread_umi

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ValueError found when run test_read.fq #8

Closed happy1219 closed 4 years ago

happy1219 commented 5 years ago

Hello, hope you are doing well. I have tested the data in test file, but below error came out:

[xxxxx - DataIndex] Loaded 1/1 (100.00%) sample files. Traceback (most recent call last): File "/home/miniconda3/envs/medaka/bin/medaka", line 11, in sys.exit(main()) File "/home/miniconda3/envs/medaka/lib/python3.6/site-packages/medaka/medaka.py", line 434, in main args.func(args) File "/home/miniconda3/envs/medaka/lib/python3.6/site-packages/medaka/stitch.py", line 120, in stitch joined = stitch_from_probs(args.inputs, regions=args.regions) File "/home/miniconda3/envs/medaka/lib/python3.6/site-packages/medaka/stitch.py", line 48, in stitch_from_probs for r in regions] File "/home/miniconda3/envs/medaka/lib/python3.6/site-packages/medaka/stitch.py", line 48, in for r in regions] File "/home/miniconda3/envs/medaka/lib/python3.6/site-packages/medaka/common.py", line 457, in from_string start = int(bounds) ValueError: invalid literal for int() with base 10: 'size=118'

Any idea/suggestions? Thanks so much.

SorenKarst commented 5 years ago

Hi!

Interesting error. The pipeline fails in the medaka polishing step possibly due to problems with parsing the sequence headers. The problem might originate earlier in the process, so can you do the following:

Please zip the folder with the results from running the test data and upload it here (i.e. tar -zcvf test_data.gz test_data/) and then I will take a look at it.

happy1219 commented 5 years ago

Hi!

Interesting error. The pipeline fails in the medaka polishing step possibly due to problems with parsing the sequence headers. The problem might originate earlier in the process, so can you do the following:

Please zip the folder with the results from running the test data and upload it here (i.e. tar -zcvf test_data.gz test_data/) and then I will take a look at it.

Hi! Thanks so much for the reply! test_data.gz version_dump.txt I have noticed you removed version dump request, but I have added it anyway. Again, thank you and waiting for your reply.

Take care,

SorenKarst commented 5 years ago

Hi again.

I had a quick look and I am pretty sure medaka fails as it interprets the colon in the sequence header as region reference (hint in the release notes for v0.10.0 https://github.com/nanoporetech/medaka/tree/v0.10.0).

You have two options. A) Downgrade medaka to version 0.7.1 B) Install the development version of the pipeline: https://github.com/SorenKarst/longread-UMI-pipeline/tree/develop. If you are using the automatic installer script you should download it from here: https://github.com/SorenKarst/longread-UMI-pipeline/blob/develop/scripts/install_dependencies.sh. and use the command bash install_dependencies.sh develop to install.

Be aware that medaka v0.10.0 on conda seems to have a minor bug that will make it crash during tensorflow https://github.com/nanoporetech/medaka/issues/100 . If this happens to you install version v0.9.2 or install without conda.

All the best

happy1219 commented 4 years ago

Hi again.

I had a quick look and I am pretty sure medaka fails as it interprets the colon in the sequence header as region reference (hint in the release notes for v0.10.0 https://github.com/nanoporetech/medaka/tree/v0.10.0).

You have two options. A) Downgrade medaka to version 0.7.1 B) Install the development version of the pipeline: https://github.com/SorenKarst/longread-UMI-pipeline/tree/develop. If you are using the automatic installer script you should download it from here: https://github.com/SorenKarst/longread-UMI-pipeline/blob/develop/scripts/install_dependencies.sh. and use the command bash install_dependencies.sh develop to install.

Be aware that medaka v0.10.0 on conda seems to have a minor bug that will make it crash during tensorflow nanoporetech/medaka#100 . If this happens to you install version v0.9.2 or install without conda.

All the best

Hi again! Option A worked. Really appreciated it. Take care,

SorenKarst commented 4 years ago

Great! Thank you for pointing this out.

I will leave the issue open until there is a permanent fix.