Error with MAJIQ (possible failure to find BAM files?)

[Huck Thornton]

Hi Paul,

Thanks for your message. As an update, based on the information you provided, my system administrator thinks he was able to install MAJIQ on a system-wide level, so let's consider the system-wide level for now. I think we might be making some progress.

I tried to use the MAJIQ build command using the following command:

majiq build /t1-data/huck/MAJIQ/annotation.gff3 -o /t1-data/huck/MAJIQ/build -c /t1-data/huck/MAJIQ/majiq_build_config2.ini

However, it didn't work. I have pasted the error message I received below.

The path to the bam files is:

/t1-data/huck/DESEQ/

Question: Do I need to have bam.bai files?

I tried used the following config files:

config file 1

[info]
bamdirs=/t1-data/huck/DESEQ
genome=hg38

[experiments]
group_a=fileA1_Aligned.out,fileA2_Aligned.out
group_b=fileB1_Aligned.out,fileB2_Aligned.out

Error message:

/package/majiq/20210108/lib/python3.8/site-packages/majiq/src/config.py:81: UserWarning: sjdirs parameter not found in config file, using "./" instead
  warnings.warn(
Traceback (most recent call last):
  File "/package/majiq/20210108/bin/majiq", line 11, in <module>
    load_entry_point('majiq==2.2', 'console_scripts', 'majiq')()
  File "/package/majiq/20210108/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 "/package/majiq/20210108/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 "/package/majiq/20210108/lib/python3.8/site-packages/majiq/src/config.py", line 35, in __new__
    Config.instance = Config.__Config(*argv)
  File "/package/majiq/20210108/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 fileA1_Aligned.out.bam in any of the provided paths in the build configuration

[Paul Jewell]

Hi Huck, 

You will need to create ".bam.bai" indexes files along with the bams. 

You can use "$ samtools index" to accomplish this (http://www.htslib.org/)

Thanks, 

-Paul

[Huck Thornton]

Hi Paul,

I made the bai files, however, I am now receiving a new error message when I run the majiq build command. It suggests that I might have an incorrect GFF.

I used the following command:

majiq build /t1-data/user/huck/MAJIQ/new_annotation.gff3 -o /t1-data/user/huck/MAJIQ/build -c /t1-data/user/huck/MAJIQ/majiq_build_config.ini

The error message is the following, for many many genes:

"2021-01-27 1:37:28,977 (PID:3860) - WARNING - Error, incorrect gff. exon doesn't have valid mRNA b'ENST00000377654.4'

2021-01-27 1:37:28,977 (PID:3860) - WARNING - Error, incorrect gff. exon doesn't have valid mRNA b'ENST00000614115.4'

2021-01-27 1:37:28,978 (PID:3860) - WARNING - Error, incorrect gff. exon doesn't have valid mRNA b'ENST00000620084.4'

2021-01-27 1:37:28,978 (PID:3860) - WARNING - Error, incorrect gff. exon doesn't have valid mRNA b'ENST00000620084.4'

2021-01-27 1:37:28,979 (PID:3860) - WARNING - Error, incorrect gff. exon doesn't have valid mRNA b'ENST00000620084.4'

Thank you again for all your help.

[Paul Jewell]

Hi Huck, 

It's not necessarily an error for a few genes, but if it's most of them, you may want to check that your annotation gene names match with your bamfile gene names. Sometimes the new versions of the annotations make slight differences in the formatting of the gene names that might need to be adjusted. 

Thanks, 

-Paul