Hello, I've seen similar problems with gtf files posted elsewhere, where the problems seem to be due to differences in the naming of the chomosomes (e.g. Chr22 vs. 22) between the gtf file and indexed genome. But my chromosomes are both called 'chr_' in my index and gtf files (I have tried gft files from both ensembl and UCSC'. Could anyone suggest a solution?
The error I get is as follows:
[2013-08-05 09:54:38] Beginning TopHat run (v2.0.9)
[2013-08-05 09:54:38] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-08-05 09:54:38] Checking for Samtools
Samtools version: 0.1.19.0
[2013-08-05 09:54:38] Checking for Bowtie index files (genome)..
[2013-08-05 09:54:38] Checking for reference FASTA file
[2013-08-05 09:54:38] Generating SAM header for /lmb/home/alexsc/bowtie2-2.1.0/indexes/genome
format: fastq
quality scale: phred33 (default)
[2013-08-05 09:54:41] Reading known junctions from GTF file
[FAILED]
[Errno 8] Exec format error
My input line is: /lmb/home/alexsc/tophat-2.0.9.OSX_x86_64/tophat2 -p 12 -G /lmb/home/alexsc/genes.gtf --b2-very-sensitive /lmb/home/alexsc/bowtie2-2.1.0/indexes/genome /lmb/home/alexsc/fqfiles/FCC2B5BACXX-HUMgvmNAARAAPEI-26_L7_1.fq
Thanks!
Alex
The error I get is as follows:
[2013-08-05 09:54:38] Beginning TopHat run (v2.0.9)
[2013-08-05 09:54:38] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-08-05 09:54:38] Checking for Samtools
Samtools version: 0.1.19.0
[2013-08-05 09:54:38] Checking for Bowtie index files (genome)..
[2013-08-05 09:54:38] Checking for reference FASTA file
[2013-08-05 09:54:38] Generating SAM header for /lmb/home/alexsc/bowtie2-2.1.0/indexes/genome
format: fastq
quality scale: phred33 (default)
[2013-08-05 09:54:41] Reading known junctions from GTF file
[FAILED]
[Errno 8] Exec format error
My input line is: /lmb/home/alexsc/tophat-2.0.9.OSX_x86_64/tophat2 -p 12 -G /lmb/home/alexsc/genes.gtf --b2-very-sensitive /lmb/home/alexsc/bowtie2-2.1.0/indexes/genome /lmb/home/alexsc/fqfiles/FCC2B5BACXX-HUMgvmNAARAAPEI-26_L7_1.fq
Thanks!
Alex
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