Tophat cannot determine record type in input file

[rxjhwlwz]

Can anyone help me? A problem of SOLid data alignment using TopHat

first, I built colorspace bowtie index

nohup bowtie-build -C genome.fa bowtiecolor &

second, I changed the name of“genome.fa” to “bowtiecolor.fa”

third, I ran

nohup tophat -C -Q -p 8 --bowtie1 --library-type=fr-secondstrand -G /c/wsy/ANN/Ensembl/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf -o /c/wsy/0/ /c/wsy/ANN/Ensembl/Homo_sapiens/Ensembl/GRCh37/Sequence/BowtieColor/bowtiecolor /e/oldstore/RNAseq/RawData/BIG_S335_20110506_FRAG_2_FW_0H_F3.csfasta /e/oldstore/RNAseq/RawData/BIG_S335_20110506_FRAG_2_FW_0H_F3_QV.qual &

but I got an error:

[2014-12-11 07:55:29] Beginning TopHat run (v2.0.10)
-----------------------------------------------
[2014-12-11 07:55:29] Checking for Bowtie
Bowtie version: 1.0.0.0
[2014-12-11 07:55:29] Checking for Samtools
Samtools version: 0.1.19.0
[2014-12-11 07:55:29] Checking for Bowtie index files (genome)..
[2014-12-11 07:55:29] Checking for reference FASTA file
[2014-12-11 07:55:29] Generating SAM header for /c/wsy/ANN/Ensembl/Homo_sapiens/Ensembl/GRCh37/Sequence/BowtieColor/bowtiecolor
Error: cannot determine record type in input file /e/oldstore/RNAseq/RawData/BIG_S335_20110506_FRAG_2_FW_0H_F3.csfasta

what is the problem? Thanks in advance for your help.

[dGho]

did you ever resolve this?

I am running into this same error. I know you asked this 2yrs ago, but do have any recollection of what was causing this or how you resolved this.