Tophat2 Error running 'long_spanning_reads':

[dvanic]

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

[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

[GiladZil]

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

[billstevens]

Thirded! Anyone else? Solutions?

[rpauly]

I am getting the same error..did you guys get a solution?
Thanks,
Rini

[fyousif]

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.

[Daehwan Kim]

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

[Estefania]

Thanks Daehwan. I had this problem and I could solved it with your last release .
Estefania
.

[jonas76]

Hi all,

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

J.

[kourosh.zarringhalam]

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

[jonas76]

Any chance of getting this fixed?
It's blocking all my projects at the moment...

[kourosh.zarringhalam]

Disabling --no-coverage-search fixed the problem for me.

[jonas76]

Still not fixed for me.

Command is this:

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:

[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...

[anamaretti]

Hi everyone,

I am having the same problem regardless the Tophat version that I use. Did someone could find the solution???

[jonas76]

Using Tophat 2.0.8 and Bowtie 2.1.0 and still same error.

[NicoBxl]

how many RAM do you have ? Try using less CPU also (like -p 8)