TopHat-Fusions Error

[fongchun]

Hi all,

Has anyone else run into this error when running TopHat-Fusions

"Error: Splice sequence retrieval failed with err =-11"

I am using the latest beta version of TopHat-Fusions (0.1.0) and a version compiled from source. The exact command I am running is:

tophat-fusion --solexa1.3-quals --library-type fr-unstranded -o A05247 -p 2 --allow-indels --no-coverage-search -r 136 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 -G ucsc.gtf bowtie_indices/hg19 reads.1.fastq reads.2.fastq

This is not some random one library error. It's happened in 5 libraries. I've emailed the creators of it, but haven't got any replies. So any help or suggestions would be greatly appreciated. Below is the full log of the error. Thanks.

[Tue Nov 8 09:58:56 2011] Beginning TopHat run (v0.1.0 (Beta))
-----------------------------------------------
[Tue Nov 8 09:58:56 2011] Preparing output location /share/lustre/gascoyne/WTSS/HL_CELL_LINES/tophat_fusions/A05247/
[Tue Nov 8 09:58:56 2011] Checking for Bowtie index files
[Tue Nov 8 09:58:56 2011] Checking for reference FASTA file
[Tue Nov 8 09:58:56 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Nov 8 09:58:56 2011] Checking for Samtools
Samtools Version: 0.1.18
[Tue Nov 8 09:59:05 2011] Checking reads
min read length: 76bp, max read length: 76bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[Tue Nov 8 11:18:00 2011] Reading known junctions from GTF file
[Tue Nov 8 11:41:07 2011] Mapping reads against hg19 with Bowtie
[Tue Nov 8 16:50:08 2011] Joining segment hits
[Tue Nov 8 17:23:26 2011] Mapping reads against hg19 with Bowtie (1/3)
[Tue Nov 8 21:08:36 2011] Mapping reads against hg19 with Bowtie (2/3)
[Wed Nov 9 00:47:34 2011] Mapping reads against hg19 with Bowtie (3/3)
[Wed Nov 9 03:33:56 2011] Mapping reads against hg19 with Bowtie
[Wed Nov 9 08:08:31 2011] Joining segment hits
[Wed Nov 9 08:42:17 2011] Mapping reads against hg19 with Bowtie (1/3)
[Wed Nov 9 12:58:22 2011] Mapping reads against hg19 with Bowtie (2/3)
[Wed Nov 9 17:26:48 2011] Mapping reads against hg19 with Bowtie (3/3)
[Wed Nov 9 21:03:10 2011] Searching for junctions via segment mapping
[Thu Nov 10 01:46:20 2011] Retrieving sequences for splices
[FAILED]
Error: Splice sequence retrieval failed with err =-11

[lshen]

My feeling, it is related to the " -G ucsc.gtf". Maybe you wan to try without using -G?

[Nicolas]

I have the same problem. From the logs, I understood that it's related to tophat-report, which crashes with a segmentation fault error. I didn't find a solution yet. (wrote to the authors, no answer...)
Please keep us updated if you do find something. I'll do the same.

[fongchun]

Ishen was right. It was the "-G ucsc.gtf" parameter that was causing the problem. I have removed that parameter and TopHat-Fusions has been able to get pass the problem. It is still running, but I will keep you guys posted if any other errors appear.

It's weird that this would be the problem. I used the "-G ucsc.gtf" parameter in a normal TopHat run and it never complained.

[papori]

Hi,
i have kind of the same error.. (also in the fusion), but diffrent number(-6)
i dont use -G.. so its not my problem..

this is my command:
./tophat -o Tophat/Sample1 -r 430 -p 10 preparereference/reference 50_se_first/1.fa

The output:

[2012-04-25 08:51:25] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-04-25 08:51:25] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.7.0
[2012-04-25 08:51:25] Checking for Samtools
Samtools version: 0.1.18.0
[2012-04-25 08:51:25] Checking for Bowtie index files
[2012-04-25 08:51:25] Checking for reference FASTA file
[2012-04-25 08:51:25] Generating SAM header for
preparereference/reference
format: fastq
quality scale: phred33 (default)
[2012-04-25 08:51:28] Preparing reads
left reads: min. length=51, count=3076259
[2012-04-25 08:52:14] Mapping left_kept_reads against reference with Bowtie
[2012-04-25 08:53:58] Mapping left_kept_reads_seg1 against reference with Bowtie (1/2)
[2012-04-25 08:54:24] Mapping left_kept_reads_seg2 against reference with Bowtie (2/2)
[2012-04-25 08:54:46] Searching for junctions via segment mapping
[2012-04-25 08:55:29] Retrieving sequences for splices
[FAILED]
Error: Splice sequence retrieval failed with err =-6

Any idea?

Thanks,
Pap

[lshen]

I got it run on human samples without -G, though results are not convincing for my data (only single reads, 57 nt--maybe too short).



/path_to/tophat-2.0.0.Linux_x86_64/tophat -o tophat_T6 --bowtie1 -p 8 --fusion-search --keep-fasta-order --no-coverage-search --bowtie1 -r 0 --fusion-anchor-length 13 --fusion-ignore-chromosomes chrM /path_to/hg19/genome T6.223.fastq


/path_to/tophat-2.0.0.Linux_x86_64//tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 0 --num-fusion-both 0 /path_to/hg19/genome

Hi,
i have kind of the same error.. (also in the fusion), but diffrent number(-6)
i dont use -G.. so its not my problem..

[papori]

The wierd thing is that i have 12 replicate of the same sample and the rest work fine(with same reference)
Moreover, when i changed the reference , all the samples work fine..
The problem is that i must have those 2 references..

The log files tail:
juncs_db.log
Loading comp35832_c0_seq1...done
Loading comp34767_c0_seq1...done
Loading ...done
./SeqAn-1.3/seqan/sequence/segment_infix.h:81 Assertion failed : data_begin_position <= data_end_position was: 377 > 376

prep_reads.log
tophat-2.0.0.Linux_x86_64/prep_reads: /lib64/libz.so.1: no version information available (required by tophat-2.0.0.Linux_x86_64/prep_reads)
prep_reads v2.0.0 (3280)
---------------------------
106649 out of 3182908 reads have been filtered out

run.log
tophat-2.0.0.Linux_x86_64/juncs_db 3 26 Approch_cufflinks_cuffdiff/Tophat/Trinity/Sample1/tmp/segment.juncs Approch_cufflinks_cuffdiff/Tophat/Trinity/Sample1/tmp/segment.insertions Approch_cufflinks_cuffdiff/Tophat/Trinity/Sample1/tmp/segment.deletions /dev/null LeechCdhit_preparereference2/LeechCdhit.fa > Approch_cufflinks_cuffdiff/Tophat/Trinity/Sample1/tmp/segment_juncs.fa

segment_juncs.log
Examining donor-acceptor pairings in comp99_c0_seq1
found 27107 potential junctions
Reported 27159 total potential splices
Reporting 356 potential deletions...
Reporting 167 potential insertions...
Reporting potential fusions...


I will very appreciate any help!?!

Pap

[DJParker]

Do you think the problem may be arising from the failed assertion (Assertion failed : data_begin_position <= data_end_position was: 377 > 376) that the start position is a higher number that the end position?

I also have this error, not sure how to get round it.

Any ideas anyone?

D