Question: Error running bowtie: .. (When I use tophat2)
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leenaehyeon • 10 wrote:
Hi
I was install bowtie2(apt-get install bowtie, bowtie2, samtools)
and version is
/usr/bin/bowtie2-align version 2.1.0
I ran tophat2 for RNA-seq mapping, but this error message popped up.
[2015-12-10 14:56:25] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2015-12-10 14:56:25] Checking for Bowtie
Bowtie version: 2.1.0.0
[2015-12-10 14:56:25] Checking for Samtools
Samtools version: 0.1.19.0
[2015-12-10 14:56:26] Checking for Bowtie index files (transcriptome)..
[2015-12-10 14:56:26] Checking for Bowtie index files (genome)..
[2015-12-10 14:56:26] Checking for reference FASTA file
[2015-12-10 14:56:26] Generating SAM header for /home/genome/Homo_sapiens/hg19
format: fastq
quality scale: phred33 (default)
[2015-12-10 14:56:36] Reading known junctions from GTF file
[2015-12-10 14:56:38] Preparing reads
left reads: min. length=20, max. length=101, 17432242 kept reads (15275 discarded)
right reads: min. length=20, max. length=101, 17439959 kept reads (7558 discarded)
[2015-12-10 15:07:27] Using pre-built transcriptome data..
[2015-12-10 15:07:32] Mapping left_kept_reads to transcriptome hg19_transcripts with Bowtie2
[FAILED]
Error running bowtie:
Error reading _ebwt[] array: 50459520, 50652672
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/bin/bowtie2-align -q -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 1 --sam-no-hd -x /home/genome/Homo_sapiens/hg19_transcripts -
my command is
tophat2 -o output -G GTFfile --transcriptome-index /home/genome/Homo_sapiens/hg19_transcripts --library-type fr-firststrand /home/genome/Homo_sapiens/hg19 sample1.fastq sample2.fastq
Before running tophat, bowtie2-build also I did.
how can I solve this Error problem?
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modified 5.2 years ago
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Ram ♦ 32k
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written
5.2 years ago by
leenaehyeon • 10