Tohat2.0.0.7 error when set bowtie2 to option (--b2-very-sensitive)

[intawat]

I got the same errror when set --b2-very-sensitive option. No probelm when i use defualt.

the errors were happen in the same step (apping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)) :

[2012-08-01 18:35:56] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-08-01 18:35:56] Checking for Bowtie
Bowtie version: 2.0.0.7
[2012-08-01 18:35:56] Checking for Samtools
Samtools version: 0.1.18.0
[2012-08-01 18:35:56] Checking for Bowtie index files
[2012-08-01 18:35:56] Checking for reference FASTA file
[2012-08-01 18:35:56] Generating SAM header for /c3se/NOBACKUP/groups/c3-sysbio/GC/tools/bowtie-0.12.8/indexes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
format: fastq
quality scale: phred33 (default)
[2012-08-01 18:36:30] Preparing reads
left reads: min. length=25, max. length=101, 29317658 kept reads (17769 discarded)
right reads: min. length=25, max. length=101, 29183210 kept reads (152217 discarded)
[2012-08-01 19:00:12] Mapping left_kept_reads to genome genome with Bowtie2
[2012-08-01 20:29:51] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
[2012-08-01 20:49:59] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
[2012-08-01 21:10:48] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
[2012-08-01 21:26:41] Mapping left_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
[2012-08-01 21:35:19] Mapping right_kept_reads to genome genome with Bowtie2
[2012-08-01 23:04:48] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/4)
[2012-08-01 23:25:23] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 (2/4)
[2012-08-01 23:48:05] Mapping right_kept_reads_seg3 to genome genome with Bowtie2 (3/4)
[2012-08-02 00:08:14] Mapping right_kept_reads_seg4 to genome genome with Bowtie2 (4/4)
[2012-08-02 00:20:07] Searching for junctions via segment mapping
[2012-08-02 00:36:37] Retrieving sequences for splices
[2012-08-02 00:39:02] Indexing splices
[2012-08-02 00:39:41] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2012-08-02 00:46:38] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2012-08-02 00:52:39] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2012-08-02 00:57:21] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2012-08-02 01:00:24] Joining segment hits
[2012-08-02 01:29:42] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
Traceback (most recent call last):
File "/c3se/users/intawat/Glenn/Seqsoft/tophat-2.0.4.Linux_x86_64/tophat", line 3948, in <module>
sys.exit(main())
File "/c3se/users/intawat/Glenn/Seqsoft/tophat-2.0.4.Linux_x86_64/tophat", line 3912, in main
user_supplied_deletions)
File "/c3se/users/intawat/Glenn/Seqsoft/tophat-2.0.4.Linux_x86_64/tophat", line 3572, in spliced_alignment
_segs_vs_J)
File "/c3se/users/intawat/Glenn/Seqsoft/tophat-2.0.4.Linux_x86_64/tophat", line 2256, in bowtie
stderr=open(bwt_logname, "w"))
IOError: [Errno 1] Operation not permitted: '/c3se/NOBACKUP/groups/c3-sysbio/GC/RNAseq/Intawat_tophat/tophat_CA1_very_sen_1/logs/bowtie.right_kept_reads_seg1.log'

The write read permittion is no problem. I dont know why ?

Inrawar