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Hello,
I'm somewhat relatively new in the NGS data analysis though i've been reading and searching a lot for the last couple of months. I've recently got a new computer to do my own analysis and set up Tophat to run before i left work last night. I came into work to find this error message on terminal:
Seems like everything ran quite nicely but something failed and all the .bed files Tophat output are all 0kb. I tried searching google but couldn't find information related to this error. Any idea what this is?
I'm somewhat relatively new in the NGS data analysis though i've been reading and searching a lot for the last couple of months. I've recently got a new computer to do my own analysis and set up Tophat to run before i left work last night. I came into work to find this error message on terminal:
Code:
[Wed Jun 15 17:27:11 2011] Beginning TopHat run (v1.3.0) ----------------------------------------------- [Wed Jun 15 17:27:11 2011] Preparing output location ./tophat_out/ [Wed Jun 15 17:27:11 2011] Checking for Bowtie index files [Wed Jun 15 17:27:11 2011] Checking for reference FASTA file Warning: Could not find FASTA file /usr/local/indexes/hg19_c.fa [Wed Jun 15 17:27:11 2011] Reconstituting reference FASTA file from Bowtie index Executing: /usr/local/bowtie-inspect /usr/local/indexes/hg19_c > ./tophat_out/tmp/hg19_c.fa [Wed Jun 15 17:30:39 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Wed Jun 15 17:30:39 2011] Checking for Samtools Samtools Version: 0.1.16 [Wed Jun 15 17:30:39 2011] Generating SAM header for /usr/local/indexes/hg19_c [Wed Jun 15 17:31:02 2011] Preparing reads format: fasta Left reads: min. length=51, count=110342407 [Wed Jun 15 18:10:02 2011] Mapping left_kept_reads against hg19_c with Bowtie [Wed Jun 15 19:13:38 2011] Processing bowtie hits [Wed Jun 15 20:41:53 2011] Mapping left_kept_reads_seg1 against hg19_c with Bowtie (1/2) [Wed Jun 15 21:38:25 2011] Mapping left_kept_reads_seg2 against hg19_c with Bowtie (2/2) [Wed Jun 15 22:21:20 2011] Searching for junctions via segment mapping [Wed Jun 15 23:13:44 2011] Retrieving sequences for splices [Wed Jun 15 23:19:01 2011] Indexing splices [Wed Jun 15 23:19:03 2011] Mapping left_kept_reads_seg1 against segment_juncs with Bowtie (1/2) [Wed Jun 15 23:23:37 2011] Mapping left_kept_reads_seg2 against segment_juncs with Bowtie (2/2) [Wed Jun 15 23:28:10 2011] Joining segment hits [Thu Jun 16 00:02:51 2011] Reporting output tracks [FAILED] Error: [Errno 2] No such file or directory [samopen] SAM header is present: 25 sequences.
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