Error STRique count

[Cesco16]

Hi @giesselmann , I think your tool is very interesting and I would like to use it. I tried to use the Docker version of the tool, but I met some errors that I did not completely understand. My data are as follows: fast5_pass: directory containing 484 .fast5 files resulting from MinKnow my_sample.bam: aligned reads by minimap2 my_config.tsv: tsv file with my own regions of interest I am running it on a PC with Windows 10.

I firstly run the docker version typing the command:

docker run -it --mount type=bind,source=$(pwd),target=/host/users/lenovo/desktop giesselmann/strique

Then, i did indexing:

python3 app/scripts/STRique.py index --recursive host/users/lenovo/desktop/my_sample/fast5_pass > host/users/lenovo/desktop/my_sample/fast5_pass/reads.fofn

When I ran the counting step:

cat host/users/lenovo/desktop/my_sample/my_sample.bam | python3 app/scripts/STRique.py count host/users/lenovo/desktop/my_sample/fast5_pass/reads.fofn app/models/r9_4_450bps.model host/users/lenovo/desktop/my_config.tsv > host/users/lenovo/desktop/my_sample/result.tsv

I got the many times following error:

[PID 61] [WARNING] Factory: Unexpected error in Worker, proceeding wiht remaining reads. Traceback (most recent call last):

File "/usr/local/lib/python3.6/dist-packages/STRique-0.4.2-py3.6-linux-x86_64.egg/STRique_lib/fast5Index.py", line 81, in __get_raw__ signal = fp[os.path.join(offset, 'Raw', s)][()]

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 "/usr/local/lib/python3.6/dist-packages/h5py/_hl/dataset.py", line 787, in getitem self.id.read(mspace, fspace, arr, mtype, dxpl=self._dxpl)

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/h5d.pyx", line 192, in h5py.h5d.DatasetID.read

File "h5py/_proxy.pyx", line 112, in h5py._proxy.dset_rw

OSError: Can't read data (can't open directory: /usr/local/hdf5/lib/plugin)

Followed by:

Could not retrieve bc752507-c038-4be3-bf31-93983f4a7ad6 from file host/users/lenovo/desktop/my_sample/fast5_pass/FAO49405_pass_c7cb835e_326.fast5.

And, after them, lot of:

10.11.2022 19:47:25 [PID 90] [ERROR] Detector: Error parsing alignment b734757f-310d-4599-aa25-f8fae95a25c1 4 0 0 * 0 0 TGCCTTCTAGTTTCAGTTACATCCATGCTCTATCTTCTGCTGGGATTACGGCATGACACACTTAAACATTTTCTTTATTTTTAATATGTTTCTTTCTTCTTCTTCTTCTTCTTTTTTTTTTTTTTTTTTTGTATTTTTAGTAGATATGGGTTTCACCATGTTGGCCAGGATAGTCTTGAACTCCTGACCTCAGGTGATCCACCTGCCTAGGCCTCCCAAAGTGCTGAGATTATGGGCGTGAGCTACCGCGTCCTGCCAGGAAATCCATTTTCTAAGTCTAACTTTTAAGCACTGTACCTTAATCCCTGAAGC ''('&(/)&%%'','&'++,&%$$$$%&31/0...+))3821.--(%$&*+&'(*(%%%%)4:9;887775,(&&%%&''(%$%,,3576---.1225570-4,022369@ADECDB;?55:?CGCG20@>6)&$%')-3D0///48;?5+,--0.''%&((8@?>52./+()((,18;<>AE>8445)'&&(+.../@A<95542352/-07781((()+++,54((((55:==4348846617:;=<:989/4.-,+,5))7>?7@@?<<=;54)'''''&&'()('&$$ rl:i:141

How can I deal with such errors? Thank you very much in advance!

[giesselmann]

Hi, looks like the vbz compression plugin is not found. There might be ways to install it on the host, but I'm not sure how to do that under Windows + Docker. I would recommend you to install the Windows Subsystem for Linux (WSL) from Microsoft and set up a basic Ubuntu for STRique (reinstall from source there). You can then follow the help/hints in #29. Sorry for the little help, I'm in a new job and can't maintain this package any longer.

[Cesco16]

Hi @giesselmann ,

thank you for the suggestion! I use a WSL (Ubuntu 20.04). I did all the steps in the installation page and, before using STRique on my data, I create a conda environment with the ont_vbz_hdf_plugin. I run index and count and they did work and successfully created the output file.

But I met another problem. I tried to run STRique again, but now I have this error message:

Traceback (most recent call last): File "STRique/scripts/STRique.py", line 49, in from STRique_lib import fast5Index, pyseqan ModuleNotFoundError: No module named 'STRique_lib'

Any ideas to solve this error? Thank you very much!