Problem with BAM files in the Majiq Build command

[Damien Plassard]

Hello,

I installed MAJIQ v2.4 as described in the installation part. Everything worked fine but when I run the majiq build command, the command seems stuck when reading the BAM file (for days, the command doesn't progress) :

2023-07-17 10:31:11,895 (PID:39134) - INFO - Majiq Build v2.4.dev102+g2cae1507
2023-07-17 10:31:11,895 (PID:39134) - INFO - Command: /shared/ifs/home/plassard/Conda/envs_conda_flash/envmajiq_2_4/bin/majiq build Homo_sapiens.GRCh38.107_UCSC_chr.gff3 -c /shared/ngs/illumina/common/project/2022/S22072/230712_A02/MAJIQ_2_4/MITF_vs_TFE3_fusions/Builder/conf.txt --output MITF_vs_TFE3_fusions/Builder --min-experiments 0.5 --minreads 3 --minpos 2 --disable-denovo --disable-denovo-ir -j 4
2023-07-17 10:31:11,895 (PID:39134) - INFO - Parsing GFF3
2023-07-17 10:31:47,490 (PID:39134) - INFO - Reading bamfiles
2023-07-17 10:31:47,502 (PID:39134) - INFO - Group MITF, number of experiments: 4, minexperiments: 2

2023-07-17 10:31:47,503 (PID:39134) - INFO - Reading bam file /shared/ngs/illumina/common/project/2022/S22072/230712_A02/MAJIQ_2_4/MITF_vs_TFE3_fusions/BAM/JNGR117.bam

Do you have any idea where this might be coming from?

Thank you in advance,

Best regards,

Damien Plassard

 

[San Jewell]

Hello,

It's a little hard to know for sure without knowing more about the system. For example are you running  this directly on a machine, in a screen session, or on a cluster grid manager?

Are you able to run a command like "top" or "glances" , in order to see if the process is stuck in a "D" state (frozen waiting for the disk/storage)? If so, there may be a physical problem with the storage media, or you might have some luck moving the bam files to scratch space or even /dev/shm.

Let me know what you see while the process is running.

Thanks,

-San

[Reza Rahman]

Dear Developer,

Thanks for building MAJIQ. I'm also facing a similar issue. I'm running job on HPC, however, the I see majiq build step has been stuck as I did not see any change in the output.

2023-10-07 14:15:44,241 (PID:3635088) - INFO - Majiq Build v2.4.dev102+g2cae1507
2023-10-07 14:15:44,241 (PID:3635088) - INFO - Command: /home/s4613408/.local/bin/majiq build /scratch/project_mnt/S0077/GFF/Mus_musculus.GRCm39.110.gff3 -o /scratch/project_mnt/S0077/out -c /scratch/project_mnt/S0077/majiq_build_config.ini -j 20
2023-10-07 14:15:44,241 (PID:3635088) - INFO - Parsing GFF3
2023-10-07 14:15:46,879 (PID:3635088) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000166255'
2023-10-07 14:15:46,884 (PID:3635088) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000095364'
2023-10-07 14:15:53,536 (PID:3635088) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000167638'
2023-10-07 14:15:53,539 (PID:3635088) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000167638'
2023-10-07 14:15:53,539 (PID:3635088) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000103301'
2023-10-07 14:15:53,539 (PID:3635088) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000103301'
2023-10-07 14:15:58,307 (PID:3635088) - INFO - Reading bamfiles
2023-10-07 14:15:58,313 (PID:3635088) - INFO - Group TTX, number of experiments: 1, minexperiments: 1
2023-10-07 14:15:58,313 (PID:3635088) - INFO - Reading bam file /scratch/project_mnt/S0077/scaling_birectional/fastq/star_align/TTX24h_1_1.fqAligned.sortedByCoord.out.bam

I'll appreciate if you kind assist me in overcoming this issue.

Best regards

Reza

[San Jewell]

Hi Reza, I would ask a similar question of you as of the last questioner. Are you able to check the process using ps, top, glances, etc and check what state it is in? R S or D? I'm imagining something is going weird with the storage as this is very strange.

Thanks,

-San

[y yang]

Hi, the state is S