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Old 02-15-2011, 12:12 AM   #1
pengchy
Senior Member
 
Location: China

Join Date: Feb 2009
Posts: 116
Default Tophat: Warning: Encountered reference sequence with only gaps

Hi,
I have encountered one problem listed as follows. The results are not influenced by this Warning. But I don't know if there are other influences. Could any one can tell me? Thanks.
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[Sun Feb 13 20:07:48 2011] Beginning TopHat run (v1.0.12)
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[Sun Feb 13 20:07:48 2011] Preparing output location /home/pengchy/tophat/tophat_out/SC_b_16h/part2/
[Sun Feb 13 20:07:48 2011] Checking for Bowtie index files
[Sun Feb 13 20:07:48 2011] Checking for reference FASTA file
[Sun Feb 13 20:07:48 2011] Checking for Bowtie
Bowtie version: 0.12.5.0
[Sun Feb 13 20:07:49 2011] Checking reads
seed length: 90bp
format: fastq
quality scale: --solexa1.3-quals
[Sun Feb 13 21:06:26 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
[Mon Feb 14 00:10:41 2011] Joining segment hits
Splitting reads into 3 segments
[Mon Feb 14 00:50:45 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
[Mon Feb 14 06:03:03 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
[Mon Feb 14 10:37:23 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
[Mon Feb 14 15:21:41 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
[Mon Feb 14 18:12:48 2011] Joining segment hits
Splitting reads into 3 segments
[Mon Feb 14 18:37:11 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
[Mon Feb 14 22:54:31 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
[Tue Feb 15 03:32:22 2011] Mapping reads against test.scafSeq.fill_FG.2 with Bowtie
[Tue Feb 15 07:34:35 2011] Searching for junctions via segment mapping
[Tue Feb 15 09:11:17 2011] Retrieving sequences for splices
[Tue Feb 15 09:16:18 2011] Indexing splices
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
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