GESS - exon skipping scanner
Entering edit mode
4.0 years ago
hinkel2 ▴ 10


I'm trying to detect exon skipping events from my RNAseq data, following the described workflow. First, I aligned my reads to reference genome using tophat2. Output bam file was sorted using samtools and used for further analysis by GESS as recommended:

python -i myfile_sorted.bam -g Arabidopsis_thaliana.TAIR10.31.dna.genome.fa -o outputfolder -n outputdata -l 5

whereafter GESS starts running

ARGUMENTS LIST: name = outputdata RNA-seq bamfile = /path/to/myfile_sorted.bam Params l = 5 INFO @ Thu, 20 Apr 2017 18:13:26: Initializing... INFO @ Thu, 20 Apr 2017 18:13:26: Constructing SpliceGraph: Intron gap linking...

However, after 5 to 10 minutes GESS stops running showing following error message:

Traceback (most recent call last): File "", line 122, in <module> main() File "", line 60, in main global_data = GESS_graphBuild(options,global_data) File "/path/to/gess/impl/", line 145, in GESS_graphBuild chr_ssgraph,chr_depthdict = ssGraphProc.process() File "/path/to/gess/impl/", line 53, in process self.chromSplicGraphMap = self.updateToDiGraph() File "/path/to/gess/impl/", line 103, in updateToDiGraph refseq = SeqIO.parse(genomedir + chrid + '.fa','fasta').next() File "/usr/lib/python2.7/dist-packages/Bio/SeqIO/", line 583, in parse with as_handle(handle, mode) as fp: File "/usr/lib/python2.7/", line 17, in __enter__ return File "/usr/lib/python2.7/dist-packages/Bio/", line 90, in as_handle with open(handleish, mode, **kwargs) as fp: IOError: [Errno 2] No such file or directory: './Pt.fa'

I have absolutely no idea what's going wrong here. Especially I dont know where the './Pt.fa' comes from. Is there someone who faced this problem before and/or could help me? :)

Thanks in advance!

gess exon-skipping RNA-Seq python • 1.1k views
Entering edit mode
3.7 years ago
adglink • 0

I think it's because some where in your bam file you have reads aligned to a chromosome referred as "Pt". So GESS is expecting there to be Pt.fa file.


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