Open: No such file or directory while running psiclass/classes

[Atari61]

Hi, I'm using PsiClass on 12 STAR bams. Stages from 0 to 3 run without any problems, but 4th throws the following error:

/storage/home/maslov/psiclass/classes  -p 28  --lb /storage/analysis/opi/transcriptome/class/bamlist.txt  -s ./subexon/psiclass_subexon_combined.out -o ./psiclass > ./psiclass_classes.log
open: No such file or directory
Segmentation fault (core dumped)
Terminated

The command I use to run PsiClass: psiclass --lb $WD/bamlist.txt --bamGroup $WD/bamgroup.txt -p 28 This error replicates when I run the classes command alone.

On the other hand, example data works just fine and doesn't throw any error.

Thank you very much for your help

[mourisl]

Could you please check whether the ./subexon/psiclass_subexon_combined.out file exists? Is there any output information in the ./psiclass_classes.log file? Thank you.

[Atari61]

./subexon/psiclass_subexon_combined.out exists and is not empty, ./psiclass_classes.log also exists but is empty.

[mourisl]

Could you please directly run "/storage/home/maslov/psiclass/classes -p 28 --lb /storage/analysis/opi/transcriptome/class/bamlist.txt -s ./subexon/psiclass_subexon_combined.out -o ./psiclass" at that folder and see what is the output on the screen?

[Atari61]

I ran it and got the same output:

/storage/home/maslov/psiclass/classes -p 28 --lb /storage/analysis/opi/transcriptome/class/bamlist.txt -s ./subexon/psiclass_subexon_combined.out -o ./psiclass
open: No such file or directory
Segmentation fault (core dumped)

Also tried to use an absolute path to psiclass_subexon_combined.out, but still the same output.

[mourisl]

For the full psiclass run, did you find other such errors in the stage of "junc" and "subexon-info"? It could be that one of the bam files in the bamlist.txt is inaccessible.

[Atari61]

No, I haven't. Just a clean run, expect the classes part: for each of the bam files in bamlist.txt there's both .splice and .rawsplice and a subexon${num}_out, at least, and they are not empty. I just have tried a set of hisat bams and got the same error and the same output.

[Atari61]

Okay, I've moved all the input to the installation dir and have run PsiClass from there and classes works now. Is such behaviour a supposed one? Or I should have been able to run it from anywhere.

[mourisl]

It should be run from anywhere. How long is each line in the bamlist.txt file? It could be the path to a bam file is too long (>1024 characters) and causes the error.

[Atari61]

Each line is 90-ish chars long.