Error while generating reports for mOTUs. (fails integration tests)
nairsajjal opened this issue · 2 comments
While doing the integration tests for the test scripts present in
https://github.com/ngless-toolkit/ngless/tree/master/tests/motus
on running
ngless motus.ngl there is an error being generated.
After running the trace --flag, the following is being observed,
[Fri 28-02-2020 12:55:51] Line 4: Running garbage collection.
[Fri 28-02-2020 12:55:51] Line 4: Interpreting [interpretIO]: input = paired("input.1.fq.gz"; second="input.2.fq.gz")
[Fri 28-02-2020 12:55:51] Line 4: Interpreting [assignment]: paired("input.1.fq.gz"; second="input.2.fq.gz")
[Fri 28-02-2020 12:55:51] Line 4: Executing paired on "input.1.fq.gz""input.2.fq.gz"""
[Fri 28-02-2020 12:55:51] Line 4: Simple Statistics completed for: input.1.fq.gz
[Fri 28-02-2020 12:55:51] Line 4: Number of base pairs: 75
[Fri 28-02-2020 12:55:51] Line 4: Encoding is: SolexaEncoding
[Fri 28-02-2020 12:55:51] Line 4: Number of sequences: 500
[Fri 28-02-2020 12:55:51] Line 4: Simple Statistics completed for: input.2.fq.gz
[Fri 28-02-2020 12:55:51] Line 4: Number of base pairs: 75
[Fri 28-02-2020 12:55:51] Line 4: Encoding is: SolexaEncoding
[Fri 28-02-2020 12:55:51] Line 4: Number of sequences: 500
[Fri 28-02-2020 12:55:51] Line 6: Running garbage collection.
[Fri 28-02-2020 12:55:51] Line 6: Interpreting [interpretIO]: mapped = map(Lookup 'input' as NGLReadSet; reference="motus")
[Fri 28-02-2020 12:55:51] Line 6: Interpreting [assignment]: map(Lookup 'input' as NGLReadSet; reference="motus")
Exiting after internal error. If you can reproduce this issue, please run your script with the --trace flag and report a bug at https://github.com/ngless-toolkit/ngless/issues
./Modules/motus.ngm/0.1/data/mOTU.v1.padded.ngless-index.lock: lock: does not exist (No such file or directory)
That's a confusing error. The issue is that the Modules folder is not found or is in the incorrect location.
Please check that the folder mentioned in the error exists. The message about the lock file not existing likely reflects that not the lock but the folder where the lock is supposed to be created doesn't exist.
The tests are currently passing on TravisCI so this is likely something affecting your installation/setup. Consider https://github.com/ngless-toolkit/ngless/blob/master/.travis.yml as reference for how to run the tests.
This no longer applies as the code has also changed internally