tophat error

nunu_ping

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Join Date: Apr 2010

Posts: 4
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tophat error

01-11-2011, 01:34 AM

Does anyone know what is wrong here? I used tophat for my RNA seq data, but error occurs...

[Mon Jan 10 22:20:48 2011] Beginning TopHat run (v1.1.4)
-----------------------------------------------
[Mon Jan 10 22:20:48 2011] Preparing output location output_dir//
[Mon Jan 10 22:20:48 2011] Checking for Bowtie index files
[Mon Jan 10 22:20:48 2011] Checking for reference FASTA file
[Mon Jan 10 22:20:48 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Jan 10 22:20:48 2011] Checking for Samtools
Samtools version: 0.1.11.0
[Mon Jan 10 22:20:55 2011] Checking reads
min read length: 76bp, max read length: 76bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[Mon Jan 10 22:34:39 2011] Mapping reads against ensembl_human_v60 with Bowtie
[Mon Jan 10 23:10:25 2011] Joining segment hits
[Tue Jan 11 01:24:08 2011] Mapping reads against ensembl_human_v60 with Bowtie(1/3)
[Tue Jan 11 01:49:37 2011] Mapping reads against ensembl_human_v60 with Bowtie(2/3)
[Tue Jan 11 02:04:24 2011] Mapping reads against ensembl_human_v60 with Bowtie(3/3)
[Tue Jan 11 02:15:54 2011] Searching for junctions via segment mapping
[Tue Jan 11 03:26:00 2011] Retrieving sequences for splices
[Tue Jan 11 03:50:25 2011] Indexing splices
[Tue Jan 11 04:38:27 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 11 05:01:24 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 11 05:19:07 2011] Mapping reads against segment_juncs with Bowtie
[Tue Jan 11 05:32:35 2011] Joining segment hits
Traceback (most recent call last):
File "/opt/sandbox/tools/tophat-1.1.4/bin/tophat", line 2223, in <module>
sys.exit(main())
File "/opt/sandbox/tools/tophat-1.1.4/bin/tophat", line 2181, in main
user_supplied_juncs)
File "/opt/sandbox/tools/tophat-1.1.4/bin/tophat", line 2053, in spliced_alignment
os.rename(merged_map, mapped_reads)
OSError: [Errno 1] Operation not permitted
Tags: None

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