Hi,
I'm trying to run majiq build, using the example from work shop, but havent got much success. The followings are:
+ The command I use:
(env_majiq_3) hugheslab@michael-Precision-Tower-3620:~$ majiq build /home/hugheslab/workshop_example_majiq/DB.gff3 --conf /home/hugheslab/workshop_example_majiq/settings.ini.txt --output build_groups
+ The error message I receive:
/home/hugheslab/env_majiq_3/lib/python3.8/site-packages/majiq/src/config.py:81: UserWarning: sjdirs parameter not found in config file, using "./" instead
warnings.warn(
/home/hugheslab/env_majiq_3/lib/python3.8/site-packages/majiq/src/config.py:89: UserWarning: "readlen" parameter is deprecated and will not be used. MAJIQ now detects the maximum read length of each experiment automatically.
warnings.warn(
Traceback (most recent call last):
File "/home/hugheslab/env_majiq_3/bin/majiq", line 33, in <module>
sys.exit(load_entry_point('majiq==2.2', 'console_scripts', 'majiq')())
File "/home/hugheslab/env_majiq_3/lib/python3.8/site-packages/majiq/run_majiq.py", line 529, in main
args.func(args)
File "majiq/src/build.pyx", line 659, in majiq.src.build.build
File "/home/hugheslab/env_majiq_3/lib/python3.8/site-packages/majiq/src/basic_pipeline.py", line 13, in pipeline_run
return pipeline.run()
File "majiq/src/build.pyx", line 668, in majiq.src.build.Builder.run
File "/home/hugheslab/env_majiq_3/lib/python3.8/site-packages/majiq/src/config.py", line 35, in __new__
Config.instance = Config.__Config(*argv)
File "/home/hugheslab/env_majiq_3/lib/python3.8/site-packages/majiq/src/config.py", line 146, in __init__
raise RuntimeError(
RuntimeError: No matching bam (and bam.bai) or sj file was found matching the experiment workshop_Adr1 in any of the provided paths in the build configuration
+ content of my config file:
[info]
readlen=101
bamdirs=/workshop_example_majiq/bam
genome= mm10
genome_path= ref_genomes_ensembl/Mus_musculus.GRCm38.dna.primary_assembly.fa
[experiments]
Adr=workshop_Adr1,workshop_Adr2,workshop_Adr3
Cer=workshop_Cer1,workshop_Cer2,workshop_Cer3
The bam & corresponding bam.bai files are located in home/hugheslab/workshop_example_majiq/bam.
The environment (env_majiq_3) is located in home/hugheslab.
I'm using ubuntu 16.04, python 3.5. The environment however is created with python3.8 -m -venv env_majiq_3. And I have no trouble running command majiq build -help, so I think I've successfully installed majiq.
I wonder what could have gone wrong and how to fix that. Thank you in advance!