View Single Post
Old 03-20-2011, 01:53 PM   #13
lei
Member
 
Location: germany

Join Date: Mar 2010
Posts: 14
Default

the econd script is :

#!/bin/bash

#PBS -N Tophat_lib1
#PBS -l nodes=1pn=8:lsdf
#PBS -l walltime=50:00:00
#PBS -l mem=5g
#PBS -M l.gu@gmail.com
#PBS -m ae
#PBS -j eo
#PBS -e /home/gu/solid/lib1/error

# environment variable for the indexes
BOWTIE_INDEXES=/home/gu/solid/bowtieIndex/
export BOWTIE_INDEXES
#reads=/home/gu/solid/lib1/138000338_20101201_FRAG_BC_SEQ0014_bcSample1_lib1_F3.csfasta
#qual=/home/gu/solid/lib1/138000338_20101201_FRAG_BC_SEQ0014_bcSample1_lib1_F3_QV.qual
#outdir= /home/gu/solid/lib1
#gtffile=/ibios/co01/hutter/PlassData/Ensembl57_transcripts_hg19.gtf

tophat --color --quals -p 8 -o /home/gu/solid/lib1 --library-type fr-secondstrand -G /ibios/co01/hutter/PlassData/Ensembl57_transcripts_hg19.gtf /icgc/lsdf/mb/analysis/hutter/bowtieIndex/hg19 /home/gu/solid/lib1/138000338_20101201_FRAG_BC_SEQ0014_bcSample1_lib1_F3.csfasta /home/gu/solid/lib1/138000338_20101201_FRAG_BC_SEQ0014_bcSample1_lib1_F3_QV.qual

the error code is :
[Thu Mar 17 16:12:28 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Thu Mar 17 16:12:28 2011] Preparing output location /home/gu/solid/lib1/
[Thu Mar 17 16:12:28 2011] Checking for Bowtie index files
[Thu Mar 17 16:12:28 2011] Checking for reference FASTA file
[Thu Mar 17 16:12:28 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Thu Mar 17 16:12:28 2011] Checking for Samtools
Samtools Version: 0.1.12a
[Thu Mar 17 16:12:28 2011] Checking reads
min read length: 50bp, max read length: 50bp
format: fasta
[Thu Mar 17 16:14:07 2011] Reading known junctions from GTF file
[Thu Mar 17 16:18:51 2011] Mapping reads against hg19 with Bowtie
[Thu Mar 17 16:18:51 2011] Joining segment hits
Traceback (most recent call last):
File "/ibios/tbi_cluster/11.0/x86_64/bin/tophat", line 2346, in <module>
sys.exit(main())
File "/ibios/tbi_cluster/11.0/x86_64/bin/tophat", line 2304, in main
user_supplied_deletions)
File "/ibios/tbi_cluster/11.0/x86_64/bin/tophat", line 1972, in spliced_alignment
segment_len)
File "/ibios/tbi_cluster/11.0/x86_64/bin/tophat", line 1545, in split_reads
reads_file = open(reads_filename)
IOError: [Errno 2] No such file or directory: '/home/gu/solid/lib1/tmp/left_kept_reads_missing.fq'
lei is offline   Reply With Quote