WARNING - Error, incorrect gff. exon doesn't have valid transcript and Intron offset 6376 miscalculated

[Xing]

Hello,

When I run the majiq, I met the following problem:

command :

majiq build  -c ./config_new.txt /data/mus/ref/ensembl/GFF3/Mus_musculus.GRCm39.104.gff3 -o ./build/  -j 30

config file:

[info]
bamdirs=/data/mus/nanopore/top3b_brain_majiq/bams
sjdirs=./sj
genome=mm10
strandness=none
[experiments]
WT=1.aln.sorted,2.aln.sorted,3.aln.sorted,4.aln.sorted
KO=5.aln.sorted,6.aln.sorted,7.aln.sorted,8.aln.sorted

Errors:

2024-07-06 17:03:44,041 (PID:1767952) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000166255'
2024-07-06 17:03:44,050 (PID:1767952) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000095364'
2024-07-06 17:03:44,193 (PID:1767952) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000103555'

.....

Intron offset 6376 miscalculated
Intron offset 12775 miscalculated
Intron offset 4429 miscalculated
Intron offset 5748 miscalculated
Intron offset 3781 miscalculated
Intron offset 3823 miscalculated
Intron offset 5180 miscalculated
.........

Any suggestions?

thank you.

[San Jewell]

Hello,

In general this indicates that something strange might have occurred in the specific experiment which yields unexpected or undefined results. I don't have a good suggestion for clearing that warning without seeing the data to determine what might have happened. Also note that this is a warning and not an error, so if the problem only affects a few genes you can use the majority of the results without an issue.

Do you think there is and chance we might be able to chat in private to check on this specific data to see what is happening?

Thank you,

-San

[Xing]

Yes, sure. Thank you. Nice to talk with you. How about July 24 10:00 am? Or you can give a time slot, I will check whether it's available for me.

Xing

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[Xing]

Hi, 

I want to say that it's not several genes but lots of genes, even hundreds to thousands. That's why I post it here and still wait for further feedback to do the following majiq analysis.

Xingliang

[San Jewell]

Hi Xingliang, I'm sorry I was away at a conference and I didn't see your initial suggestion fast enough.

Would you or folks you work with be opposed to transferring a subset of the data to us for review, so that we can reproduce and debug the specific cause of this issue? If so I can communicate privately with you to arrange it.

Thanks,

-San

[Xing]

Hi, San,

Do you have an alternative email to receive the data? It seems this email doesn't work well. I've sent several emails but no response. I don't want to show the data in public right now as well.

Xingliang

[San Jewell]

Hi Xingliang, I will contact you outside the thread, thanks.

[Rezanur Rahman]

Hi there

I am facing the same error. After running for 10 hours I see the following errors:

2024-10-25 13:19:56,272 (PID:2700798) - INFO - Majiq Build v2.4.dev102+g2cae1507
2024-10-25 13:19:56,272 (PID:2700798) - INFO - Command: /home/s4613408/.local/bin/majiq build -c ./majiq_build_config.ini -o ./build --disable-ir --disable-denovo --disable-denovo-ir -j 40 ./Mus_musculus.GRCm39.110.gff3
2024-10-25 13:19:56,276 (PID:2700798) - INFO - Parsing GFF3
2024-10-25 13:19:59,808 (PID:2700798) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000166255'
2024-10-25 13:19:59,814 (PID:2700798) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000095364'
2024-10-25 13:20:08,599 (PID:2700798) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000167638'
2024-10-25 13:20:08,599 (PID:2700798) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000167638'
2024-10-25 13:20:08,600 (PID:2700798) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000103301'
2024-10-25 13:20:08,600 (PID:2700798) - WARNING - Error, incorrect gff. exon doesn't have valid transcript b'transcript:ENSMUST00000103301'
2024-10-25 13:20:14,713 (PID:2700798) - INFO - Reading bamfiles
2024-10-25 13:20:14,716 (PID:2700798) - INFO - Group CTR, number of experiments: 2, minexperiments: 1
2024-10-25 13:20:14,716 (PID:2700798) - INFO - Reading bam file /scratch/project_mnt/S0077/project_Sam68_scaling/majiq/FG12-Ctr1.sorted.bam
slurmstepd: error: *** JOB 11329182 ON bun062 CANCELLED AT 2024-10-25T23:50:11 DUE TO TIME LIMIT ***

The command I used:

majiq build -c ./majiq_build_config.ini \
            -o ./build \
            --disable-ir --disable-denovo --disable-denovo-ir -j 40 \
            ./Mus_musculus.GRCm39.110.gff3

Could you please suggest the possible solution of this problem?

I appreciate your time.

Kind regards

Reza

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.

[San Jewell]

Hi Reza,

For future reference, please create a new thread when asking a new question. (so as not to ping the original author with many messages)

In general, seeing some lines with the "exon doesn't have valid transcript" warning, isn't fatal or a big cause for concern. Some annotations just don't provide transcripts for some exon rows but most of the data is still usable, and from this text, I don't think you should be concerned.

However, your main problem here is just that you are in a slurm interactive (or batch, it's hard to tell from this alone) compute job, which took longer than the time you allocated on the scheduler. This is unrelated to majiq itself. Please see documentation for slurm ; for example, you can add a flag to "srun" or "sbatch" like -t 2-0 , which will ask for two days of runtime.

Let me know if it helps.

Thanks,

-San