Error in majiq v2 deltapsi when generating voila files

[Pedro Barbosa]

Hello,

I'm trying out majiq2 v2.1-c3da3ce to analyse splicing changes in a time-course experiment. However, issues appeared when writing output files.

Please find below the output as well as the command used.

Any help?

Best,

Pedro

majiq deltapsi --nproc 20 -o dpsi_t12_vs_t0 \

--mem-profile \

-n t0 t12 \

-grp1 $PWD/myC_time0_rep1_Aligned.sortedByCoord.out.majiq \

$PWD/myC_time0_rep2_Aligned.sortedByCoord.out.majiq \

$PWD/myC_time0_rep3_Aligned.sortedByCoord.out.majiq -grp2  $PWD/myC_time12_rep1_Aligned.sortedByCoord.out.majiq \

$PWD/myC_time12_rep2_Aligned.sortedByCoord.out.majiq \

$PWD/myC_time12_rep3_Aligned.sortedByCoord.out.majiq

```Start Computing DeltaPSI

2019-09-17 13:06:19,804 (PID:84111) - INFO - Computation done, saving results....

Traceback (most recent call last):

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/voila/api/matrix_hdf5.py", line 65, in add_dataset

    grp = grp[k]

  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper

  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/h5py/_hl/group.py", line 264, in __getitem__

    oid = h5o.open(self.id, self._e(name), lapl=self._lapl)

  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper

  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper

  File "h5py/h5o.pyx", line 190, in h5py.h5o.open

KeyError: "Unable to open object (file read failed: time = Tue Sep 17 13:06:23 2019\n, filename = 'dpsi_t12_vs_t0/t0_t12.deltapsi.voila', file descriptor = 5, errno = 5, error message = 'Input/output error', buf = 0x55e86cc7a720, total read size = 512, bytes this sub-read = 512, bytes actually read = 18446744073709551615, offset = 0)"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/bin/majiq", line 10, in <module>

    sys.exit(main())

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/majiq/run_majiq.py", line 204, in main

    args.func(args)

  File "majiq/src/deltapsi.pyx", line 27, in majiq.src.deltapsi.deltapsi

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/majiq/src/basic_pipeline.py", line 11, in pipeline_run

    return pipeline.run()

  File "majiq/src/deltapsi.pyx", line 202, in majiq.src.deltapsi.DeltaPsi.run

  File "majiq/src/deltapsi.pyx", line 140, in majiq.src.deltapsi._core_deltapsi

  File "majiq/src/deltapsi.pyx", line 178, in majiq.src.deltapsi._core_deltapsi

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/voila/api/matrix_hdf5.py", line 381, in add

    self.matrix_hdf5.add_multiple(self.lsv_id, **kwargs)

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/voila/api/matrix_hdf5.py", line 92, in add_multiple

    self.add(lsv_id, key, value)

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/voila/api/matrix_hdf5.py", line 80, in add

    self.add_dataset(self.LSVS, gene_id, lsv_id, key, data=data)

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/voila/api/matrix_hdf5.py", line 67, in add_dataset

    grp = grp.create_group(k)

  File "/home/pedro.barbosa/software/miniconda3/envs/majiq/lib/python3.7/site-packages/h5py/_hl/group.py", line 68, in create_group

    gid = h5g.create(self.id, name, lcpl=lcpl, gcpl=gcpl)

  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper

  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper

  File "h5py/h5g.pyx", line 161, in h5py.h5g.create

ValueError: Unable to create group (name already exists)

```

[Paul Jewell]

Hi Pedro, 

From both the "input/output error" and name already exists error, I would guess that the issue may be a hardware fault in the disk. Could you perhaps try to output to an empty location on a separate storage volume to verify if this makes any difference?

Thanks, 

-Paul

[Pedro Barbosa]

Dear Paul,

Indeed, by directing the output into a separate storage volume it seems to work :)

Thanks