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Old 08-12-2012, 05:29 PM   #1
dvanic
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Unhappy Tophat2 Error running 'long_spanning_reads':

Hi!
I'm getting an error running Tophat 2.0.4 on 100bp PE illumina reads without a reference transcriptome to map to (same dataset, with reference gtf, completes happily).
The error I'm getting is

Quote:
[2012-08-11 23:10:13] Joining segment hits
[FAILED]
Error running 'long_spanning_reads':Loading insertions...done
What could be the cause of this???

Thanks in advance,
Dee
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Old 10-12-2012, 12:31 AM   #2
GiladZil
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Default Tophat Error running 'long_spanning_reads'

I got exactly the same with Tophat 2.0.5.
In addition, I got the warnings: " no version information available".
Does anybody have a solution?

Cheers,
Gilad
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Old 10-15-2012, 08:36 AM   #3
billstevens
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Thirded! Anyone else? Solutions?
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Old 10-16-2012, 05:30 AM   #4
rpauly
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I am getting the same error..did you guys get a solution?
Thanks,
Rini
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Old 10-16-2012, 09:29 AM   #5
fyousif
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I am getting the same error with 2.0.5. Only 2 out of the 10 samples I have tried to process went through successfully. A core file is being dumped in the Tophat output folder and re-running the command with -R always results in the same error.
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Old 10-22-2012, 10:55 AM   #6
Daehwan Kim
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We fixed this problem in an unofficial version TopHat v2.0.6, which we will release sometime soon. If you want to give it a try, it is available at:
http://tophat.cbcb.umd.edu/downloads/

Thanks,
Daehwan
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Old 10-26-2012, 05:12 AM   #7
Estefania
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Thanks Daehwan. I had this problem and I could solved it with your last release .
Estefania
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Old 12-18-2012, 08:48 AM   #8
jonas76
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Hi all,

I'm using 2.0.6 and I'm still getting this error. Any ideas?
Running Linux 64 bit binaries.

J.
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Old 01-05-2013, 06:25 PM   #9
kourosh.zarringhalam
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Hi,

I have the same problem. I am using TopHat v2.0.6 linux 64 binaries. Aligning to mm10 (with bowtie2). Here is the output:

[2013-01-04 09:37:50] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-01-04 09:37:50] Checking for Bowtie
Bowtie version: 2.0.2.0
[2013-01-04 09:37:50] Checking for Samtools
Samtools version: 0.1.18.0
[2013-01-04 09:37:50] Checking for Bowtie index files
[2013-01-04 09:37:50] Checking for reference FASTA file
[2013-01-04 09:37:50] Generating SAM header for /home/kouroshz/Genomes/mm10
format: fastq
quality scale: phred33 (default)
[2013-01-04 09:38:20] Preparing reads
left reads: min. length=66, max. length=66, 33701679 kept reads (88722 discarded)
right reads: min. length=66, max. length=66, 33628059 kept reads (162342 discarded)
[2013-01-04 10:03:57] Mapping left_kept_reads to genome mm10 with Bowtie2
[2013-01-04 11:09:43] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/2)
[2013-01-04 11:25:08] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/2)
[2013-01-04 12:21:07] Mapping right_kept_reads to genome mm10 with Bowtie2
[2013-01-04 13:24:13] Mapping right_kept_reads_seg1 to genome mm10 with Bowtie2 (1/2)
[2013-01-04 13:38:34] Mapping right_kept_reads_seg2 to genome mm10 with Bowtie2 (2/2)
[2013-01-04 14:32:38] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) if this step takes too much time or memory.
[2013-01-05 19:08:42] Retrieving sequences for splices
[2013-01-05 19:11:42] Indexing splices
[2013-01-05 19:41:44] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2013-01-05 19:53:02] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2013-01-05 20:27:56] Joining segment hits
[FAILED]
Error running 'long_spanning_reads':Loading insertions...done


kz
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Old 01-11-2013, 08:24 PM   #10
jonas76
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Any chance of getting this fixed?
It's blocking all my projects at the moment...
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Old 01-21-2013, 09:52 AM   #11
kourosh.zarringhalam
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Disabling --no-coverage-search fixed the problem for me.
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Old 01-22-2013, 04:15 AM   #12
jonas76
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Still not fixed for me.

Command is this:

Code:
tophat2 --output-dir CT_0603.tophat -p 20 --no-coverage-search --keep-fasta-order -zpigz --transcriptome-index=/switchlab/group/tools/RNASeq/GTF/Homo_sapiens_assembly19 -G /switchlab/group/tools/RNASeq/GTF/Homo_sapiens.GRCh37.67-chr-added.gtf /switchlab/group/tools/RNASeq/GTF/Homo_sapiens_assembly19 CT_0603.Short_read.lane2.120608FCB.fastq_clean
Output:

Code:
[2013-01-22 00:39:35] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-01-22 00:39:35] Checking for Bowtie
		  Bowtie version:	 2.0.4.0
[2013-01-22 00:39:44] Checking for Samtools
		Samtools version:	 0.1.18.0
[2013-01-22 00:39:44] Checking for Bowtie index files
[2013-01-22 00:39:44] Checking for Bowtie index files
[2013-01-22 00:39:44] Checking for reference FASTA file
[2013-01-22 00:39:44] Generating SAM header for /switchlab/group/tools/RNASeq/GTF/Homo_sapiens_assembly19
	format:		 fastq
	quality scale:	 phred33 (default)
[2013-01-22 00:43:21] Reading known junctions from GTF file
[2013-01-22 00:43:45] Preparing reads
	 left reads: min. length=20, max. length=51, 21472529 kept reads (2268 discarded)
[2013-01-22 00:48:50] Using pre-built transcriptome index..
[2013-01-22 00:53:46] Mapping left_kept_reads to transcriptome Homo_sapiens_assembly19 with Bowtie2 
[2013-01-22 01:25:38] Resuming TopHat pipeline with unmapped reads
[2013-01-22 01:25:41] Mapping left_kept_reads.m2g_um to genome Homo_sapiens_assembly19 with Bowtie2 
[2013-01-22 01:31:07] Mapping left_kept_reads.m2g_um_seg1 to genome Homo_sapiens_assembly19 with Bowtie2 (1/2)
[2013-01-22 01:39:42] Mapping left_kept_reads.m2g_um_seg2 to genome Homo_sapiens_assembly19 with Bowtie2 (2/2)
[2013-01-22 01:46:26] Searching for junctions via segment mapping
[2013-01-22 02:09:30] Retrieving sequences for splices
[2013-01-22 02:12:47] Indexing splices
[2013-01-22 02:13:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2013-01-22 02:13:15] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2013-01-22 02:13:29] Joining segment hits
	[FAILED]
Error running 'long_spanning_reads':Loading insertions...done
Getting desperate...
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Old 02-04-2013, 12:51 PM   #13
anamaretti
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Default Hi everyone,

I am having the same problem regardless the Tophat version that I use. Did someone could find the solution???
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Old 03-25-2013, 01:31 AM   #14
jonas76
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Using Tophat 2.0.8 and Bowtie 2.1.0 and still same error.
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Old 03-25-2013, 02:21 AM   #15
NicoBxl
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how many RAM do you have ? Try using less CPU also (like -p 8)
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Old 03-27-2013, 06:34 AM   #16
jonas76
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I have 8GB of RAM per job/slot I run on our cluster. So when I submit -p 8, I enable 64GB of RAM since I also open 8 slots then.
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Old 04-26-2013, 12:56 PM   #17
chanwu
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Question Tophat2 error

Hello, everyone,

I am a newer to use Tophat2/bowtie2 to align illumina paired-end RNA-seq, and a error occured as
No such file or directory.
Can someone help out to solve this problem? thanks,

Chanwu
command used:

tophat -o 81MAGABXX_5PE hg19 /media/sf_F_DRIVE/finished/81MAGABXX_5_R1.fastq /media/sf_F_DRIVE/finished/81MAGABXX_5_R2.fastq



[2013-04-23 10:13:59] Beginning TopHat run (v2.0.8)
-----------------------------------------------
[2013-04-23 10:13:59] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-04-23 10:14:00] Checking for Samtools
Samtools version: 0.1.18.0
[2013-04-23 10:14:00] Checking for Bowtie index files
[2013-04-23 10:14:00] Checking for reference FASTA file
[2013-04-23 10:14:00] Generating SAM header for hg19
format: fastq
quality scale: phred33 (default)
[2013-04-23 10:14:34] Preparing reads
left reads: min. length=100, max. length=100, 87918264 kept reads (261507 discarded)
right reads: min. length=100, max. length=100, 87900059 kept reads (279712 discarded)
[2013-04-23 11:00:31] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-04-24 01:54:58] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4)
[2013-04-24 03:07:58] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/4)
[2013-04-24 04:21:15] Mapping left_kept_reads_seg3 to genome hg19 with Bowtie2 (3/4)
[2013-04-24 05:43:19] Mapping left_kept_reads_seg4 to genome hg19 with Bowtie2 (4/4)
[2013-04-24 07:03:11] Mapping right_kept_reads to genome hg19 with Bowtie2
[2013-04-25 02:02:18] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4)
[2013-04-25 03:12:53] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/4)
[2013-04-25 04:21:35] Mapping right_kept_reads_seg3 to genome hg19 with Bowtie2 (3/4)
[2013-04-25 06:20:24] Mapping right_kept_reads_seg4 to genome hg19 with Bowtie2 (4/4)
[2013-04-25 07:37:57] Searching for junctions via segment mapping
[2013-04-25 09:42:00] Retrieving sequences for splices
[2013-04-25 09:43:50] Indexing splices
[2013-04-25 09:46:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2013-04-25 10:09:23] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2013-04-25 10:33:07] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2013-04-25 10:57:47] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2013-04-25 11:20:03] Joining segment hits
[2013-04-25 11:58:22] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2013-04-25 12:21:21] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2013-04-25 12:42:55] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2013-04-25 13:10:07] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2013-04-25 13:30:45] Joining segment hits
[2013-04-25 14:17:03] Reporting output tracks
[FAILED]
Error: [Errno 2] No such file or directory
Found 313015 junctions from happy spliced reads
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