Hi, all
When using tophat commands, I am confronted with the following errors.
[root@** bin]# /home/bin/tophat -p 8 -G Ptrichocarpa_156_gene.gff3 -o CAR01 --max-intron-length 5000 -r 150 -m 2 --solexa1.3-quals /home/bin/bowtie-0.12.8/indexes/Pop_trichocarpa /home/****/Fastq/CAR01_1.fastq /home/****/Fastq/CAR01_2.fastq
[2012-05-22 10:24:03] Beginning TopHat run (v2.0.1)
-----------------------------------------------
[2012-05-22 10:24:03] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.8.0
[2012-05-22 10:24:03] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-22 10:24:03] Checking for Bowtie index files
[2012-05-22 10:24:03] Checking for reference FASTA file
[2012-05-22 10:24:03] Generating SAM header for /home/bin/bowtie-0.12.8/indexes/Pop_trichocarpa
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[2012-05-22 10:24:03] Reading known junctions from GTF file
[2012-05-22 10:24:05] Preparing reads
[FAILED]
Error running 'prep_reads'
terminate called after throwing an instance of 'int'
I cannot figure out the problem. I am wondering about the flag " --solexa1.3-quals". Our reads are generated by Illumia Hi-seq. So, I assume it is >= 1.3. Is that right?
Any comments and suggestions are very appreciated.
When using tophat commands, I am confronted with the following errors.
[root@** bin]# /home/bin/tophat -p 8 -G Ptrichocarpa_156_gene.gff3 -o CAR01 --max-intron-length 5000 -r 150 -m 2 --solexa1.3-quals /home/bin/bowtie-0.12.8/indexes/Pop_trichocarpa /home/****/Fastq/CAR01_1.fastq /home/****/Fastq/CAR01_2.fastq
[2012-05-22 10:24:03] Beginning TopHat run (v2.0.1)
-----------------------------------------------
[2012-05-22 10:24:03] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.8.0
[2012-05-22 10:24:03] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-22 10:24:03] Checking for Bowtie index files
[2012-05-22 10:24:03] Checking for reference FASTA file
[2012-05-22 10:24:03] Generating SAM header for /home/bin/bowtie-0.12.8/indexes/Pop_trichocarpa
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[2012-05-22 10:24:03] Reading known junctions from GTF file
[2012-05-22 10:24:05] Preparing reads
[FAILED]
Error running 'prep_reads'
terminate called after throwing an instance of 'int'
I cannot figure out the problem. I am wondering about the flag " --solexa1.3-quals". Our reads are generated by Illumia Hi-seq. So, I assume it is >= 1.3. Is that right?
Any comments and suggestions are very appreciated.
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