Zero LSV found also bam files are not recognized

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Praveenkumar R

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Apr 21, 2024, 3:20:10 PMApr 21
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Dear Developers,

I'm trying to use MAJIQ. 

My config file:

[info]
bamdirs=/home/praveenkumar/MAJIQQ/bam
genome=Homo
genome_path=/home/praveenkumar/reference_genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa
strandness=None
[experiment]
WT=WT_1
KO=KO_1

2024-04-21 21:02:58,369 (PID:27263) - INFO - ╔═══════════════════════════════════════════════════════════════╗

2024-04-21 21:02:58,369 (PID:27263) - INFO - ╠╡ ACADEMIC License applied                                 

2024-04-21 21:02:58,369 (PID:27263) - INFO -   Name: Official Majiq Academic-only License                  

2024-04-21 21:02:58,369 (PID:27263) - INFO -   File: majiq_license_academic_official.lic                   

2024-04-21 21:02:58,369 (PID:27263) - INFO -   Expiration Date: Never                                      

2024-04-21 21:02:58,370 (PID:27263) - INFO -                                                               

2024-04-21 21:02:58,370 (PID:27263) - INFO - ╠╡ The academic license is for non-commercial purposes by      

2024-04-21 21:02:58,370 (PID:27263) - INFO - ╠╡ individuals at an academic or not for profit institution.   

2024-04-21 21:02:58,370 (PID:27263) - INFO - ╚═══════════════════════════════════════════════════════════════╝

2024-04-21 21:03:00,936 (PID:27263) - INFO - Parsing GFF3

2024-04-21 21:04:08,223 (PID:27263) - INFO - Adding Transcript Exons

2024-04-21 21:04:18,144 (PID:27263) - INFO - Reading bamfiles

2024-04-21 21:04:18,145 (PID:27263) - INFO - Detecting LSVs ngenes: 58051

2024-04-21 21:04:37,729 (PID:27263) - INFO - 0 LSV found

2024-04-21 21:04:40,141 (PID:27263) - INFO - MAJIQ Builder is ended successfully!


I have no clue why it not running.

2024-04-21 21:02:57,877 (PID:27263) - INFO - Majiq Build v2.5.6.dev1+g8423f68b

Command: /home/praveenkumar/Majiq_env_test/bin/majiq build /home/praveenkumar/reference_annotation/Homo_sapiens_GRCh38_86_con_from_gtf.gff3 -o /home/praveenkumar/MAJIQQ/output -c /home/praveenkumar/MAJIQQ/config_test.ini

My bam files and indexed files are in the same directory also my configure file.

i checked the gff file chromosome names are 1,2,3 like in my bam file. 


Can you please help me with this. Thanks in advance.





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