Problem during run and during unitest.sh

[desmodus1984]

Hi, I installed the gpu version of nanoreviser, and everything supposedly when ok, but the unitest.sh failed: (nanorev) [jpac1984@o0311 nanoreviser]$ sh unitest.sh Traceback (most recent call last): File "NanoReviser.py", line 26, in from albacore.path_utils import get_default_path ModuleNotFoundError: No module named 'albacore' Traceback (most recent call last): File "NanoReviser_train.py", line 25, in from albacore.path_utils import get_default_path ModuleNotFoundError: No module named 'albacore' Traceback (most recent call last): File "./unitest/check_nanoreviser.py", line 26, in with open(log_fn, 'r') as lg: FileNotFoundError: [Errno 2] No such file or directory: './unitest/unitest_log.txt' unitest has been completed.

Also, then I thought, that I might have been the case of the test, so I tried running a test with some real data, and it failed too. Here is the command line: (nanorev) [jpac1984@o0311 nanoreviser]$ python NanoReviser.py -d /fs/scratch/PHS0338/MDA-T7-BC05/ -o ./MDA-T7-BC05/ -S human -F fastq Traceback (most recent call last): File "NanoReviser.py", line 26, in from albacore.path_utils import get_default_path ModuleNotFoundError: No module named 'albacore'

Thanks;

[Christoph-Ammer]

Hi I also faced the same problem. I installed albacore after downloading from official ONT webpage with following commant python -m pip install ont_albacore-2.3.4-cp36-cp36m-manylinux1_x86_64.whl Processing ./ont_albacore-2.3.4-cp36-cp36m-manylinux1_x86_64.whl Hope that helps!! Best

[Christoph-Ammer]

sorry the command was only python -m pip install ont_albacore-2.3.4-cp36-cp36m-manylinux1_x86_64.whl afterwards I ran python NanoReviser.py -d ./unitest/test_data/fast5/ -o ./unitest_nanorev_results/ -S ecoli -F fastq and it worked.

[desmodus1984]

Well. It doesn't help much. I have processed my reads with Guppy not with Albacore which is not supported nor recommended by ONT.

Get BlueMail for Androidhttp://www.bluemail.me/r?b=16117 On Jan 12, 2021, at 05:36, Christoph-Ammer <[email protected]mailto:[email protected]> wrote:

Hi I also faced the same problem. I installed albacore after downloading from official ONT webpage with following commant python -m pip install ont_albacore-2.3.4-cp36-cp36m-manylinux1_x86_64.whl Processing ./ont_albacore-2.3.4-cp36-cp36m-manylinux1_x86_64.whl Hope that helps!! Best

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[Christoph-Ammer]

I agree! But the tool just works with albacore. Also in their paper the authors did not include analysis with guppy. I will try to compare the results from nanoreviser with these from guppy and if I do not see any significant differences I will stick to the official workflow from ONT --> guppy:-)