Jit
Enthusiast computational biologist with business dream !!!
Our Sponsors
Install Bwise using conda !
By Jit 1191 days ago
(JitMetaENV) ➜ test_phase_assebly conda install -c bioconda bwise
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/urbe/anaconda3/envs/JitMetaENV
added / updated specs:
- bwise
The following packages will be downloaded:
package | build
---------------------------|-----------------
bcalm-2.2.3 | h2e03b76_2 4.6 MB bioconda
bgreat-2.0.0 | h2e03b76_3 143 KB bioconda
btrim-1.0.1 | h7d875b9_3 48 KB bioconda
bwise-1.0.0 | h2e03b76_1 11 KB bioconda
certifi-2021.5.30 | py36h5fab9bb_0 141 KB conda-forge
------------------------------------------------------------
Total: 4.9 MB
The following NEW packages will be INSTALLED:
bcalm bioconda/linux-64::bcalm-2.2.3-h2e03b76_2
bgreat bioconda/linux-64::bgreat-2.0.0-h2e03b76_3
btrim bioconda/linux-64::btrim-1.0.1-h7d875b9_3
bwise bioconda/linux-64::bwise-1.0.0-h2e03b76_1
The following packages will be UPDATED:
ca-certificates 2021.4.13-h06a4308_1 --> 2021.7.5-h06a4308_1
certifi 2020.12.5-py36h5fab9bb_1 --> 2021.5.30-py36h5fab9bb_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
certifi-2021.5.30 | 141 KB | ####################################################################### | 100%
bcalm-2.2.3 | 4.6 MB | ####################################################################### | 100%
bwise-1.0.0 | 11 KB | ####################################################################### | 100%
btrim-1.0.1 | 48 KB | ####################################################################### | 100%
bgreat-2.0.0 | 143 KB | ####################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(JitMetaENV) ➜ test_phase_assebly bwise
*** This is BWISE - High order De Bruijn graph assembler ***
The command line was: /home/urbe/anaconda3/envs/JitMetaENV/bin/bwise
[Warning] /home/urbe/JitSimuStudy/test_phase_assebly directory already exists, BWISE will use it.
Results will be stored in: /home/urbe/JitSimuStudy/test_phase_assebly
usage: bwise [-h] [-x PAIRED_READFILES] [-u SINGLE_READFILES]
[-s KMER_SOLIDITY] [-S KMER_COVERAGE] [-p SR_SOLIDITY]
[-P SR_COVERAGE] [-k K_MIN] [-K K_MAX] [-e MAPPING_EFFORT]
[-a ANCHOR_SIZE] [-i FRACTION_ANCHOR] [-A MAX_OCCURENCE]
[-m MISSMATCH_ALLOWED] [-g GREEDY_K2000] [-t NB_CORES]
[-o OUT_DIR] [-H HAPLO_MODE] [--version]
[FATAL ERROR] BWISE requires at least a read file
To find out why, try `Bwise --help` and/or check the logs files of the various steps of the pipeline (logs/logBloo coo, logs/logBcalm, logs/logTips, logs/logBgreat, logs/logK2000).
