Hi Folks:
I met a problem while aligning RNA-seq data with tophat.
It shows like this:
[Wed Oct 5 17:10:55 2011] Beginning TopHat run (v1.3.2)
-----------------------------------------------
[Wed Oct 5 17:10:55 2011] Preparing output location ./tophat_out/
[Wed Oct 5 17:10:55 2011] Checking for Bowtie index files
[Wed Oct 5 17:10:55 2011] Checking for reference FASTA file
[Wed Oct 5 17:10:55 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Oct 5 17:10:55 2011] Checking for Samtools
Samtools Version: 0.1.18
[Wed Oct 5 17:10:55 2011] Generating SAM header for /mydata/data/personal_data/maize-genome/chr1_seg_index/chr1_seg_index
[Wed Oct 5 17:10:55 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
Left reads: min. length=96, count=18982267
[Wed Oct 5 18:26:16 2011] Mapping left_kept_reads against chr1_seg_index with Bowtie
[Wed Oct 5 18:53:45 2011] Processing bowtie hits
[Wed Oct 5 21:13:26 2011] Mapping left_kept_reads_seg1 against chr1_seg_index with Bowtie (1/4)
[Wed Oct 5 21:46:18 2011] Mapping left_kept_reads_seg2 against chr1_seg_index with Bowtie (2/4)
[Wed Oct 5 22:19:09 2011] Mapping left_kept_reads_seg3 against chr1_seg_index with Bowtie (3/4)
[Wed Oct 5 22:52:10 2011] Mapping left_kept_reads_seg4 against chr1_seg_index with Bowtie (4/4)
[Thu Oct 6 00:06:52 2011] Searching for junctions via segment mapping
[Thu Oct 6 00:14:24 2011] Retrieving sequences for splices
[Thu Oct 6 00:14:28 2011] Indexing splices
[Thu Oct 6 00:14:30 2011] Mapping left_kept_reads_seg1 against segment_juncs with Bowtie (1/4)
[Thu Oct 6 00:25:11 2011] Mapping left_kept_reads_seg2 against segment_juncs with Bowtie (2/4)
[Thu Oct 6 00:35:50 2011] Mapping left_kept_reads_seg3 against segment_juncs with Bowtie (3/4)
[Thu Oct 6 00:46:29 2011] Mapping left_kept_reads_seg4 against segment_juncs with Bowtie (4/4)
[Thu Oct 6 01:02:16 2011] Joining segment hits
[Thu Oct 6 01:06:06 2011] Reporting output tracks
[FAILED]
Error: [Errno 2] No such file or directory
[samopen] SAM header is present: 1 sequences.
Does any one know what happened and how to fix it?
Thanks a lot
Tao
I met a problem while aligning RNA-seq data with tophat.
It shows like this:
[Wed Oct 5 17:10:55 2011] Beginning TopHat run (v1.3.2)
-----------------------------------------------
[Wed Oct 5 17:10:55 2011] Preparing output location ./tophat_out/
[Wed Oct 5 17:10:55 2011] Checking for Bowtie index files
[Wed Oct 5 17:10:55 2011] Checking for reference FASTA file
[Wed Oct 5 17:10:55 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Oct 5 17:10:55 2011] Checking for Samtools
Samtools Version: 0.1.18
[Wed Oct 5 17:10:55 2011] Generating SAM header for /mydata/data/personal_data/maize-genome/chr1_seg_index/chr1_seg_index
[Wed Oct 5 17:10:55 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
Left reads: min. length=96, count=18982267
[Wed Oct 5 18:26:16 2011] Mapping left_kept_reads against chr1_seg_index with Bowtie
[Wed Oct 5 18:53:45 2011] Processing bowtie hits
[Wed Oct 5 21:13:26 2011] Mapping left_kept_reads_seg1 against chr1_seg_index with Bowtie (1/4)
[Wed Oct 5 21:46:18 2011] Mapping left_kept_reads_seg2 against chr1_seg_index with Bowtie (2/4)
[Wed Oct 5 22:19:09 2011] Mapping left_kept_reads_seg3 against chr1_seg_index with Bowtie (3/4)
[Wed Oct 5 22:52:10 2011] Mapping left_kept_reads_seg4 against chr1_seg_index with Bowtie (4/4)
[Thu Oct 6 00:06:52 2011] Searching for junctions via segment mapping
[Thu Oct 6 00:14:24 2011] Retrieving sequences for splices
[Thu Oct 6 00:14:28 2011] Indexing splices
[Thu Oct 6 00:14:30 2011] Mapping left_kept_reads_seg1 against segment_juncs with Bowtie (1/4)
[Thu Oct 6 00:25:11 2011] Mapping left_kept_reads_seg2 against segment_juncs with Bowtie (2/4)
[Thu Oct 6 00:35:50 2011] Mapping left_kept_reads_seg3 against segment_juncs with Bowtie (3/4)
[Thu Oct 6 00:46:29 2011] Mapping left_kept_reads_seg4 against segment_juncs with Bowtie (4/4)
[Thu Oct 6 01:02:16 2011] Joining segment hits
[Thu Oct 6 01:06:06 2011] Reporting output tracks
[FAILED]
Error: [Errno 2] No such file or directory
[samopen] SAM header is present: 1 sequences.
Does any one know what happened and how to fix it?
Thanks a lot
Tao
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