Error while running RNASeq-MATS.py-File "RNASeq-MATS.py", line 204, in <module> myLen=int(output); ValueError: invalid literal for int() with base 10

[Miriam]

Hi,

I'm new to rMATS and fairly new to RNA-Seq analysis. I was trying to run a test with my bam-files, that are paired-end reads, that have been mapped using tophat2 and I'm using rMATS.3.0.9. The error that I get is:

Traceback (most recent call last):
  File "RNASeq-MATS.py", line 204, in <module>
    myLen=int(output);
ValueError: invalid literal for int() with base 10: 'Usage:   samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\nOptions: -b       output BAM\n         -h       print header for the SAM output\n         -H       print header only (no alignments)\n '


and this is my code for running rMATS:

python RNASeq-MATS.py -b1 ../../../new-data/ml439/trimmed/alignment/SC_1/SC_1_accepted_hits.bam, ../../../new-data/ml439/trimmed/alignment/SC_2/SC_2_accepted_hits.bam,../../../new-data/ml439/trimmed/alignment/SC_3/SC_3_accepted_hits.bam -b2 ../../../new-data/ml439/trimmed/alignment/T_7/T_7_accepted_hits.bam, ../../../new-data/ml439/trimmed/alignment/T_8/T_8_accepted_hits.bam,../../../new-data/ml439/trimmed/alignment/T_9/T_9_accepted_hits.bam -gtf ../../../new-data/ml439/stringtie/Rat_stringtie_15june2015_merged.sorted.processed.gtf -o SCvsT_test -t paired -len 101 >& SCvsT_test/errlogfile

I have searched in forums about the error, and it seems that it's a problem where the command finds a string but can't convert it into an integer. The problem is I don't know that does it mean in my context and more importantly how can i solve it. I would appreciate if someone could help.

Thank you very much!

Miriam

[Juw Won Park]

Hello,

It's probably from samtools version conflict. Please use v0.1.19 (http://sourceforge.net/projects/samtools/files/samtools/0.1.19/) until we take care of this in the next version of rMATS.

Best,

Juw Won

[Miriam]

Hi,

I've just checked and the version I'm using for samtools is : Version: 0.1.19-44428cd. So it seems I'm using the version you're recommending. Any other suggestions?

Thanks

[Juw Won Park]

Did you run rMATS with qsub? If so, can you double check the version of samtools installed on the compute nodes? 

-Juw Won

[Miriam]

I'm sorry but I'm afraid I don't know what you mean by "Did you run rMATS with qsub? ".  I'm running rMATS in a server and when I've typed samtools this is what i get:

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd

Usage:   samtools <command> [options]
.....

I can double check with the server administrator if that helps,
Thank you,

On Tuesday, 13 October 2015 10:25:02 UTC+1, Miriam wrote: