Majiq build

[Haoyi Wu]

Hello, I encountered some issues during the majiq build process. I have checked my paths and files and did not find any errors. Below are the commands I used and the file details. Could you please help me identify where the problem might be? Your assistance would be greatly appreciated.

$majiq build /home/wuhy/data/genome_data/China_perl_data/pasa2.longest.filter.gff3 -o /home/wuhy/data/MAJIQ/MAJIQ_Builder/build -c new_2.ini --disable-denovo --disable-denovo-ir -j 40
 

Traceback (most recent call last):
  File "/home/wuhy/anaconda3/envs/majiq_env/bin/majiq", line 8, in <module>
    sys.exit(main())
  File "/home/wuhy/anaconda3/envs/majiq_env/lib/python3.10/site-packages/rna   _majiq/run_majiq.py", line 641, in main
    args.func(args)
  File "rna_majiq/src/build.pyx", line 649, in rna_majiq.src.build.build
  File "/home/wuhy/anaconda3/envs/majiq_env/lib/python3.10/site-packages/rna   _majiq/src/basic_pipeline.py", line 13, in pipeline_run
    return pipeline.run()
  File "rna_majiq/src/build.pyx", line 656, in rna_majiq.src.build.Builder.r   un
  File "/home/wuhy/anaconda3/envs/majiq_env/lib/python3.10/site-packages/rna   _majiq/src/config.py", line 35, in __new__
    Config.instance = Config.__Config(*argv)
  File "/home/wuhy/anaconda3/envs/majiq_env/lib/python3.10/site-packages/rna   _majiq/src/config.py", line 179, in __init__
    raise RuntimeError(
RuntimeError: No matching bam (and bam.bai) was found matching the experimen   t S778_1.bam in any of the provided paths in the build configuration

$less new_2.ini
[info]
bamdirs=/home/wuhy/data/MAJIQ/china_bam/Together
genome=NA
[experiments]
MN=S778_1.bam,S778_1.bam.bai,S779_1.bam,S779_1.bam.bai,S784_1.bam,S784_1.bam.bai,S795_1.bam,S795_1.bam.bai,S804_1.bam,S804_1.bam.bai,S818_2.bam,S818_2.bam.bai,S819_2.bam,S819_2.bam.bai,S820_2.bam,S820_2.bam.bai,S822_2.bam,S822_2.bam.bai,S823_2.bam,S823_2.bam.bai,S824_3.bam,S824_3.bam.bai,S825_3.bam,S825_3.bam.bai,S827_3.bam,S827_3.bam.bai,S829_3.bam,S829_3.bam.bai,S833_4.bam,S833_4.bam.bai,S836_4.bam,S836_4.bam.bai,S837_4.bam,S837_4.bam.bai,S842_4.bam,S842_4.bam.bai
LA=S808_1.bam,S808_1.bam.bai,S809_1.bam,S809_1.bam.bai,S810_1.bam,S810_1.bam.bai,S811_2.bam,S811_2.bam.bai,S812_2.bam,S812_2.bam.bai,S813_1.bam,S813_1.bam.bai,S814_1.bam,S814_1.bam.bai,S815_2.bam,S815_2.bam.bai,S816_2.bam,S816_2.bam.bai,S817_2.bam,S817_2.bam.bai,S821_3.bam,S821_3.bam.bai,S826_3.bam,S826_3.bam.bai,S838_3.bam,S838_3.bam.bai,S850_3.bam,S850_3.bam.bai,S851_3.bam,S851_3.bam.bai

$ ls /home/wuhy/data/MAJIQ/china_bam/Together

S778_1.bam      S804_1.bam      S811_2.bam      S815_2.bam      S819_2.bam      S823_2.bam      S827_3.bam      S836_4.bam      S850_3.bam
S778_1.bam.bai  S804_1.bam.bai  S811_2.bam.bai  S815_2.bam.bai  S819_2.bam.bai  S823_2.bam.bai  S827_3.bam.bai  S836_4.bam.bai  S850_3.bam.bai
S779_1.bam      S808_1.bam      S812_2.bam      S816_2.bam      S820_2.bam      S824_3.bam      S828_3.bam      S837_4.bam      S851_3.bam
S779_1.bam.bai  S808_1.bam.bai  S812_2.bam.bai  S816_2.bam.bai  S820_2.bam.bai  S824_3.bam.bai  S828_3.bam.bai  S837_4.bam.bai  S851_3.bam.bai
S784_1.bam      S809_1.bam      S813_1.bam      S817_2.bam      S821_3.bam      S825_3.bam      S829_3.bam      S838_3.bam
S784_1.bam.bai  S809_1.bam.bai  S813_1.bam.bai  S817_2.bam.bai  S821_3.bam.bai  S825_3.bam.bai  S829_3.bam.bai  S838_3.bam.bai
S795_1.bam      S810_1.bam      S814_1.bam      S818_2.bam      S822_2.bam      S826_3.bam      S833_4.bam      S842_4.bam
S795_1.bam.bai  S810_1.bam.bai  S814_1.bam.bai  S818_2.bam.bai  S822_2.bam.bai  S826_3.bam.bai  S833_4.bam.bai  S842_4.bam.bai

[San Jewell]

Hello Haoyi,

It is a simple issue, it's simply that you list out the experiments without the extensions in the config file. For example

Instead of:

MN=S778_1.bam,S778_1.bam.bai

Write:

MN=S778_1

The ".bam" and ".bam.bai" will be found by the software after just listing the files without the extension.

Let me know if it makes sense, thanks!

-San