tophat failed: Warning: junction database is empty!
Hi everyone
I embedded tophat command in a perl script. When running the script, I found a tophat failure error. I searched similar problem posts, but none of them were resolved
- http://seqanswers.com/forums/showthread.php?t=41021
- http://seqanswers.com/forums/showthread.php?t=27454
- Tophat Warning: Junction Database Is Empty!
Could you please provide me some advice? I appreciate any of your answers. THANKS
Error message:
[2015-03-01 18:02:45] Searching for junctions via segment mapping
Warning: junction database is empty!
[2015-03-01 18:02:45] Reporting output tracks
[FAILED]
Error running /usr/local/tophat/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-
... ...
FASTQ file:
@read:C:Chr1:m:29063581:29064263:267 length=100
CACTGGTGATCAGATTGAAGTTCTTAGCAACGGAAGCTGGTGAACCATGGTATTCCATTGGAGCTTCTAAATAAGGTGAAGAAGCTGAGCTCAGATTGCT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@read1
AGGAACTTGATTAGCAAAATCTCCAAGGATTATGTGAAGCTaCTCAAGTATGGTGATTCTTTGTACCGCTGCAATTGTTCCCAATGGGAAGGAGTTCGTT
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@read2
ACTCTCAGGTACCAAGTCATTGATACCCCCGGGATTTTGGATAGGCCCTTCCATGCGAAGCTCTCTGCAATCATTGACGACTTGCTGCTCTTGGTCGTAC
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
Reference File:
>genome
aagaaaaaggcacacacatttatattcaaaaactaagaacataggtcacacaagaaagattcatacatcacatggcaaaacaaaaaaaaacaaaaaaatataaagcctggagagcagatgccaaatttttaactatataatttggcatttatagcttaagagaaaatacataatgggtgtagataaaacagtgatagtactgtaaaaataaataaaatagtacatTTAGAGAGACTTTACAGCTAGAAAACGAGGCTCTTTAGGCATGAACTTCTGGTTTGCATAAACATCCATGTAATCTCCAAACACAAACTTTGGATACTTCTTCTCACTTCCTTCCTCTTCCGCCACCGCGGCTGGCCCTATCGCCGCCTTGTACGACGGATTGTAGAAGGAAGCTATAGACCTTCTGTTTCCTTCCTCCCTCGCCAACACCCTGTGCCACGCACTCTTGTACctgccaaccacattttggttaaaactttatactcaaaattgtatattttgtactagtgttgtcgtcgtgtcaccactgtttccggatcaagtcgagattagtgttttggttcgtaaaagatgagtgaaaaatacCTTCCGTTGCTAAGAACTTCAATCTGATCACCAGTGTTGATAACAATGGCATTAGGTAGAGGCTGAACATCGATCCACTCGCCGTCTTTCAAGACCTGAAGGCCATCATATTCATCGTCTTGGAAAAGCAAAACGACACCTCCTGCATCAGTATGAGCTCGAAGGCCATTGACTAGCTCAGGATGAGGACAAGGAGGGTAATGGCTGACTTTAGTCCCAAAGAAAGCTGTCTCTTCTCCATCTTCCATTCCTTCATTGAAAGCTTTCTTTATGTAACCTTTAGGCAAACCCAAATTCTCATCCATCACTTCCATCATCTTGCTCGCTAGCTTCCTCACTTCTTCTCTGTATTCTCCCATAGTCTCTctgtttttacgtacaaatagaaaaacacaaaggtgagatttttgaaaatgggtttgaaagattttgactagttttaaaagagaaaatgtttacTTAATGTTGGATGGCCATTCGTTTTGGTTATGGTCCAAGAGAGTGAAGACATCTTCCCAGTCCACGTTTTCTAGCTTCTCGCCAGAGTTCTTTTGAACCAATTCGTTGAGCAACTTCACGGGATTAGAAGTCTTGAATGCTTCTTCTCTCTCTGTTTTGTAGCAATCTGAGCTCAGCTTCTTCACCTTATTTAGAAGCTCCAATGGAATACCATGGTTCACCAGctacatacatacacagataagcacatgaaaacagagagacagagagagtgtgtgttctgttttttgttagttagatccgaacCTGAAAAAATCCCCACTCTTCGCAAGCTCTAGCGATTTCAGACAGTGTCTTCTCTCTTTCTTCACCATTGAGTTTGGAGAAATCGATAACAGGAATCGCCATttcagatccgcaaagagagagagagagacagatgtgtttttggcaagtcaaaaaagactctgtttagtagtaatcttctgatttagttgt
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Can you post the exact commands?
My command is
Can you run just
bowtie2and see what happens?Running bowtie2 (
bowtie2 -x INDEX -U in.fq -S out.sam)is OK. THANKS!I am not suggesting you to run bowtie2. I just wanted to know if bowtie2 fails. If its RNA-Seq data and you are aligning to reference genome instead of transcriptome, you should use splice aware aligner like tophat2.
Which genome it is ?
Hi Geeky, it is my test data, which contains only one sequence. I have run true data, and tophat works now. However, I am still confused of the error in testing.