Comments (2)
i could solve it, it looks like the python version of the environments was not high enough with 3.6, now with 3.9 its works.
from duplex-tools.
I also tried with the venv approach, but got the following error:
(base) sheucke@PTH2D537:/nanopore/tests$ . venv/bin/activate/nanopore/tests$ pip install duplex_tools
(duplex) (base) sheucke@PTH2D537:
Collecting duplex_tools
Downloading https://files.pythonhosted.org/packages/18/d4/d1290091cb3f5d3541edc98456749b3a2aba24327768a1cb95757df10b5c/duplex_tools-0.2.20.tar.gz
Collecting edlib (from duplex_tools)
Downloading https://files.pythonhosted.org/packages/08/a3/37558fb19e54e40e360c8f3e255007d19f262c45298bf3148b92faf3311c/edlib-1.3.9-cp36-cp36m-manylinux1_x86_64.whl (304kB)
100% |████████████████████████████████| 307kB 21.1MB/s
Collecting mappy (from duplex_tools)
Downloading https://files.pythonhosted.org/packages/9b/41/52391258e16bcc8182ddf3133d86408ed17d8d8fd6e30eea4960df29b64b/mappy-2.24.tar.gz (140kB)
100% |████████████████████████████████| 143kB 80.8MB/s
Collecting matplotlib (from duplex_tools)
Downloading https://files.pythonhosted.org/packages/09/03/b7b30fa81cb687d1178e085d0f01111ceaea3bf81f9330c937fb6f6c8ca0/matplotlib-3.3.4-cp36-cp36m-manylinux1_x86_64.whl (11.5MB)
100% |████████████████████████████████| 11.5MB 4.2MB/s
Collecting more-itertools (from duplex_tools)
Downloading https://files.pythonhosted.org/packages/0b/ff/1ad78678bee731ae5414ea5e97396b3f91de32186028daa614d322ac5a8b/more_itertools-8.14.0-py3-none-any.whl (52kB)
100% |████████████████████████████████| 61kB 57.3MB/s
Collecting natsort (from duplex_tools)
Downloading https://files.pythonhosted.org/packages/3e/58/61c4b4fd9e597affdcd3347d5991fa5be404af26f19932d3116b67e133da/natsort-8.2.0-py3-none-any.whl
Collecting numpy (from duplex_tools)
Downloading https://files.pythonhosted.org/packages/45/b2/6c7545bb7a38754d63048c7696804a0d947328125d81bf12beaa692c3ae3/numpy-1.19.5-cp36-cp36m-manylinux1_x86_64.whl (13.4MB)
100% |████████████████████████████████| 13.4MB 3.8MB/s
Collecting pandas (from duplex_tools)
Downloading https://files.pythonhosted.org/packages/c3/e2/00cacecafbab071c787019f00ad84ca3185952f6bb9bca9550ed83870d4d/pandas-1.1.5-cp36-cp36m-manylinux1_x86_64.whl (9.5MB)
100% |████████████████████████████████| 9.5MB 8.5MB/s
Collecting parasail (from duplex_tools)
Downloading https://files.pythonhosted.org/packages/6d/fd/4696ce6a2e6ed2029dc4e1964f8cd68ffd693ed7a4f9aaf6c1990f355f0b/parasail-1.3.3.tar.gz (82kB)
100% |████████████████████████████████| 92kB 61.5MB/s
Collecting pod5 (from duplex_tools)
Could not find a version that satisfies the requirement pod5 (from duplex_tools) (from versions: )
No matching distribution found for pod5 (from duplex_tools)
You are using pip version 18.1, however version 21.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(duplex) (base) sheucke@PTH2D537:~/nanopore/tests$
from duplex-tools.
Related Issues (20)
- Unexpected input file name changes output file file name format on split_on_adapter HOT 1
- Cannot install duplex_tools HOT 2
- split_pairs not working HOT 3
- pairs.txt file empty, but pairs_from_bam/pair_ids.txt not empty HOT 1
- empty output from split_pairs HOT 5
- KeyError: 'sequence_length_template' when basecalling is turned off HOT 2
- Duplicate reads and read splitting option in MinKNOW HOT 9
- Positional arguments (especially seqkit_stats_nosecondary) in duplex_tools assess_split_on_adapter HOT 1
- split_pod5 supported seed types error HOT 3
- pod5 version of duplex_tools issue HOT 3
- question on split pairs HOT 3
- promethion good pairs: 0 HOT 3
- Extracting duplex reads for multiplexed samples HOT 2
- Unexpected base in duplex call HOT 4
- issue with split_on_adapter output HOT 17
- couldn't install on linux or pc HOT 5
- np.bool deprecated, package no longer works HOT 1
- split_on_adapter no more than one core?
- guppy_duplex ValueError: not enough values to unpack (expected 4, got 3) HOT 5
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from duplex-tools.