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Old 02-08-2010, 02:04 AM   #1
yasu
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Location: Japan

Join Date: Jul 2009
Posts: 10
Question tophat running problem

Hi all,

I'm trying to run mRNA-seq for human by tophat (v1.0.12).
I succeeded to get proper output file in the preliminary dataset (first 100K reads from each .fq file). But I failed to get proper output in the real dataset (each contains ~17M reads).

I would appreciate any help you could give me with this.

Thanks in advance.

-Yasu

### preliminary_test ###

$ tophat -r 10 -p 8 -o tophat_hg19_test hg19 s_1_1.head4000000.fq,s_6_1.head4000000.fq,s_7_1.head4000000.fq s_1_2.head4000000.fq,s_6_2.head4000000.fq,s_7_2.head4000000.fq

[Mon Feb 8 13:31:03 2010] Beginning TopHat run (v1.0.12)
-----------------------------------------------
[Mon Feb 8 13:31:03 2010] Preparing output location tophat_hg19_test/
[Mon Feb 8 13:31:03 2010] Checking for Bowtie index files
[Mon Feb 8 13:31:03 2010] Checking for reference FASTA file
[Mon Feb 8 13:31:03 2010] Checking for Bowtie
Bowtie version: 0.11.3.0
[Mon Feb 8 13:31:03 2010] Checking reads
seed length: 43bp
format: fastq
quality scale: --phred33-quals
[Mon Feb 8 13:31:51 2010] Mapping reads against hg19 with Bowtie
[Mon Feb 8 13:34:24 2010] Joining segment hits
[Mon Feb 8 13:34:59 2010] Mapping reads against hg19 with Bowtie
[Mon Feb 8 13:37:30 2010] Joining segment hits
[Mon Feb 8 13:38:04 2010] Searching for junctions via segment mapping
[Mon Feb 8 13:44:59 2010] Retrieving sequences for splices
[Mon Feb 8 13:46:42 2010] Indexing splices
[Mon Feb 8 13:47:58 2010] Mapping reads against segment_juncs with Bowtie
[Mon Feb 8 13:48:47 2010] Joining segment hits
[Mon Feb 8 13:49:26 2010] Mapping reads against segment_juncs with Bowtie
[Mon Feb 8 13:50:15 2010] Joining segment hits
[Mon Feb 8 13:50:52 2010] Reporting output tracks
-----------------------------------------------
Run complete [00:33:58 elapsed]


### real_data ###

tophat -r 10 -p 8 -o tophat_hg19 hg19 s_1_1.fq,s_6_1.fq,s_7_1.fq s_1_2.fq,s_6_2.fq,s_7_2.fq

[Mon Feb 8 14:24:47 2010] Beginning TopHat run (v1.0.12)
-----------------------------------------------
[Mon Feb 8 14:24:47 2010] Preparing output location tophat_hg19/
[Mon Feb 8 14:24:47 2010] Checking for Bowtie index files
[Mon Feb 8 14:24:47 2010] Checking for reference FASTA file
[Mon Feb 8 14:24:47 2010] Checking for Bowtie
Bowtie version: 0.11.3.0
[Mon Feb 8 14:24:47 2010] Checking reads
seed length: 43bp
format: fastq
quality scale: --phred33-quals
[Mon Feb 8 14:39:23 2010] Mapping reads against hg19 with Bowtie
[Mon Feb 8 15:24:40 2010] Joining segment hits
[Mon Feb 8 15:35:38 2010] Mapping reads against hg19 with Bowtie
[Mon Feb 8 16:18:44 2010] Joining segment hits
[Mon Feb 8 16:18:44 2010] Searching for junctions via segment mapping
Warning: junction database is empty!
[Mon Feb 8 18:01:42 2010] Joining segment hits
[Mon Feb 8 18:11:38 2010] Joining segment hits
[Mon Feb 8 18:11:38 2010] Reporting output tracks
[FAILED]
Error: Report generation failed with err = 1
Traceback (most recent call last):
File "/bin/tophat", line 1518, in ?
sys.exit(main())
File "/bin/tophat", line 1490, in main
params.gff_annotation)
File "/bin/tophat", line 936, in compile_reports
exit(1)
TypeError: 'str' object is not callable
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