BHT creation not working

[Jiacheng-Git]

"There are 58051 distinct gene ID in the gtf file
There are 198002 distinct transcript ID in the gtf file
There are 36227 one-transcript genes in the gtf file
There are 1182163 exons in the gtf file
There are 24969 one-exon transcripts in the gtf file
There are 22488 one-transcript genes with only one exon in the transcript
Average number of transcripts per gene is 3.410828
Average number of exons per transcript is 5.970460
Average number of exons per transcript excluding one-exon tx is 6.687707
Average number of gene per geneGroup is 7.693822

==========
Done processing each gene from dictionary to compile AS events
Found 80401 exon skipping events
Found 12380 exon MX events
Found 14606 alt SS events
There are 8812 alt 3 SS events and 5794 alt 5 SS events.
Found 5945 RI events
Segmentation fault (core dumped)"

This is what I got when I put my data in the three lines of code "Darts_BHT rmats_count --b1 /path/to/b1.bam --b2 /path/to/b2.bam
--gtf /path/to/gtfFile.gtf --od outDir -t paired
--nthread 8 --readLength 150"
that allows me to do rMAT count. Could you please tell me what is wrong?

[zj-zhang]

Hi @Jiacheng-Git
Based on the information you provided, I won't be able to tell what exactly is the issue. I would recommend using the test dataset from rMATS website/using standalone rMATS to perform the counting step if the integrated version in DARTS_BHT does not work for you.
You can find the test data for rMATS here: http://rnaseq-mats.sourceforge.net/user_guide.htm#test

[NotValdemaras]

I get the same error with the test data as mentioned here. Would you have any insight what could be the problem?

Darts_BHT rmats_count --b1 b1.txt --b2 b2.txt --gtf Homo_sapiens.GRCh38.99.gtf -t paired --od outDir --readLength 50

There are 60676 distinct gene ID in the gtf file
There are 227818 distinct transcript ID in the gtf file
There are 36763 one-transcript genes in the gtf file
There are 1376499 exons in the gtf file
There are 25269 one-exon transcripts in the gtf file
There are 22508 one-transcript genes with only one exon in the transcript
Average number of transcripts per gene is 3.754664
Average number of exons per transcript is 6.042099
Average number of exons per transcript excluding one-exon tx is 6.671126
Average number of gene per geneGroup is 8.463790

Done processing each gene from dictionary to compile AS events
Found 49179 exon skipping events
Found 4059 exon MX events
Found 16616 alt SS events
There are 10094 alt 3 SS events and 6522 alt 5 SS events.
Found 6995 RI events

Segmentation fault (core dumped)

Update: Just some extra info. rMATS works fine in my environment (I am running it on windows WSL), however I cannot find what causes the issue when I run darts_bht.

[huzitu]

I got the same error.
The problem may be the outdir is nor existed. When I created the outdir and re-run the command, it worked.
Hope this will help.