Fail to open .bam files from STAR alignment

[Elizabeth Alice Bonner]

I am using STAR aligned sorted bam files on my organizations cluster with rMATS-turbo. My .txt files containing my bam groups are using absolute paths to each file separated by comas on one line. when I run my code I get:

gtf: 18.30930256843567
There are 60675 distinct gene ID in the gtf file
There are 232024 distinct transcript ID in the gtf file
There are 36826 one-transcript genes in the gtf file
There are 1429266 exons in the gtf file
There are 25157 one-exon transcripts in the gtf file
There are 22523 one-transcript genes with only one exon in the transcript
Average number of transcripts per gene is 3.824046
Average number of exons per transcript is 6.159992
Average number of exons per transcript excluding one-exon tx is 6.787496
Average number of gene per geneGroup is 8.484364
statistic: 0.03467059135437012

Fail to open    path/to/bamfile (x #of bam files)

I have tried to fix the problem based on the thread I was reading and amended my .txt file, but cannot figure out what is going on. Any help would be greatly appreciated

[kutsc...@gmail.com]

It sounds like you are already using the explicit path names, but similar reports in the past had to do with using "~" in the path for the home directory: https://github.com/Xinglab/rmats-turbo/issues/166

One thing you could try is running "samtools view /path/to/bam" just to see if samtools has any issue with the file

If you are able to build rMATS from the source code, then you can modify this line and re-compile to get a better error message: https://github.com/Xinglab/rmats-turbo/commit/9fceff89c8ba48647a70fba54c810ce01a572754

Eric

[Elizabeth Alice Bonner]

it looks like sam tools is able to read my path/to/bamfile , but appending ~ has not helped

[kutsc...@gmail.com]

Just to double check, the paths are expected to cause an error if they include "~" like this from the linked github issue:

Fail to open ~/workspace/rnaseq/results/GSE107958/sca_bs5.Aligned.sortedByCoord.out.bam

But the error should not happen with the ~ replaced with the full path name like:
/home/ha-na/workspace/rnaseq/results/GSE107958/sca_bs5.Aligned.sortedByCoord.out.bam

Eric