Hi all,
I'm running TOPHAT 1.0.7 with 75bp solexa reads in a pipeline that worked in the previous version - this is my command-line:
And output:
Tue May 19 13:30:36 2009] Beginning TopHat run (v1.0.7)
-----------------------------------------------
[Tue May 19 13:30:36 2009] Preparing output location ./tophat_out/
[Tue May 19 13:30:36 2009] Checking for Bowtie index files
[Tue May 19 13:30:36 2009] Checking for reference FASTA file
[Tue May 19 13:30:36 2009] Checking for Bowtie
Bowtie version: 0.9.9.3
[Tue May 19 13:30:36 2009] Checking reads
seed length: 75bp
format: fastq
quality scale: solexa
Splitting reads into 3 segments
[Tue May 19 13:30:36 2009] Mapping reads against mm9 with Bowtie
[Tue May 19 13:33:44 2009] Mapping reads against mm9 with Bowtie
[Tue May 19 13:33:47 2009] Mapping reads against mm9 with Bowtie
[Tue May 19 13:33:50 2009] Searching for junctions via coverage islands
[FAILED]
Error: segment-based junction search failed
The segment_juncs.log ends with this line:
Loading left segment hits...Error: reference sequence for ID 1621485109
, not found, aborting
Any suggestions are appreciated,
Thank you in advance,
JW, Uni. of Copenhagen
I'm running TOPHAT 1.0.7 with 75bp solexa reads in a pipeline that worked in the previous version - this is my command-line:
Code:
tophat --p 3 --solexa-quals --max-gene-family 1 /Index/mm9 /Reads/reads.fq
Tue May 19 13:30:36 2009] Beginning TopHat run (v1.0.7)
-----------------------------------------------
[Tue May 19 13:30:36 2009] Preparing output location ./tophat_out/
[Tue May 19 13:30:36 2009] Checking for Bowtie index files
[Tue May 19 13:30:36 2009] Checking for reference FASTA file
[Tue May 19 13:30:36 2009] Checking for Bowtie
Bowtie version: 0.9.9.3
[Tue May 19 13:30:36 2009] Checking reads
seed length: 75bp
format: fastq
quality scale: solexa
Splitting reads into 3 segments
[Tue May 19 13:30:36 2009] Mapping reads against mm9 with Bowtie
[Tue May 19 13:33:44 2009] Mapping reads against mm9 with Bowtie
[Tue May 19 13:33:47 2009] Mapping reads against mm9 with Bowtie
[Tue May 19 13:33:50 2009] Searching for junctions via coverage islands
[FAILED]
Error: segment-based junction search failed
The segment_juncs.log ends with this line:
Loading left segment hits...Error: reference sequence for ID 1621485109
, not found, aborting
Any suggestions are appreciated,
Thank you in advance,
JW, Uni. of Copenhagen
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