tophat2 errors

[NicoBxl]

Tophat 2 also hangs forever in

[2012-04-13 03:41:33] Searching for junctions via segment mapping

and in the segment_juncs.log

>> Performing segment-search:
Loading left segment hits...

[vyellapa]

I did'nt include the fusion flags and it worked ok. Is anybody seeing any significant speedup compared to 1.4.1? I dont.

time tophat2 -p 8 -r 50 --mate-std-dev 50 --transcriptome-index=./tophat2_transcript/GRCh37_E66 -o ./t2 \
-n 2 -N 4 --b2-sensitive --library-type fr-unstranded \
--rg-id ID000 --rg-sample M123 --rg-library lib0000 --rg-platform-unit IlluminaLn7 --rg-center TGen \
$RESOURCES/bowtie2/GRCh37.62 ./1mr1.fastq ./1mr2.fastq

[westerman]

Yes, the updated version also solved the problems I was having with crashes and hangs in the 'Joining segment' part of the program. My samples are being mapped to a non-standard organism that has over 80 scaffolds.

[NateP]

There are quite a few different problems reported in this thread - I apologize for them. We are aware of a couple of these problems and we are trying to fix them, though we are encountering some difficulties reproducing some of these errors.
We just updated the packages on the website with a couple of last minute fixes so please re-download the tophat-2.0.0 package of your choice (yes, it's the same version, same file names) from http://tophat.cbcb.umd.edu and try running the new version again on your test data. If tophat 2 still fails at any stage in the process please report the failure at [email protected] - it would also help if you attach a tarball or zip file with the content of the "logs" directory when you post a bug report there.

Thank you,
-Geo

The updated version fixed the error I posted earlier in the thread. Thank you for the quick work!

[gpertea]

There are quite a few different problems reported in this thread - I apologize for them. We are aware of a couple of these problems and we are trying to fix them, though we are encountering some difficulties reproducing some of these errors.
We just updated the packages on the website with a couple of last minute fixes so please re-download the tophat-2.0.0 package of your choice (yes, it's the same version, same file names) from http://tophat.cbcb.umd.edu and try running the new version again on your test data. If tophat 2 still fails at any stage in the process please report the failure at [email protected] - it would also help if you attach a tarball or zip file with the content of the "logs" directory when you post a bug report there.

Thank you,
-Geo

[plabaj]

I have a simillar problem at the same stage:
[FAILED]
Error: segment-based junction search failed with err =-6
Error: invalid 'B' array subtype (B)!

and TopHat was run with the following parameters:
--bowtie1 --report-secondary-alignments --bowtie-n

[Nicolas]

Same here. Tophat2 hangs forever at the same step "Searching for junctions via segment mapping", with paired-end HiSeq fastq reads (~140M reads), with or without --fusion-search option.
I ran it succesfully on a small subset of the same files (1M reads), so I suspect it has to deal with data size / memory...
Hope for a quick fix!

[ahmetz]

yeah, and i also removed fusion detection completely but they all end up giving the same error.

[Jon_Keats]

Have you tried the fusion version with the -bowtie1 option as suggested when you are doing the fusion detection.

[NateP]

I've had an error pop about at the same point when I gave it a test run the other day myself.
Was single end mapping.
Went through the left_kept_reads then:
[timestamp] Searching for junctions via segment mapping
[timestamp] Retrieving sequences for splices
[FAILED]
Error: Splice sequence retrieval failed with err =-6

[ahmetz]

now that we have tophat2 out the door, i'm sure we'll have bunch of tophat2 related error messages and solutions - hopefully.

thank you to the team for releasing the new version. i'm very excited for the combination of tophat and tophat-fusion.

now my problem. I've downloaded and installed bowtie2 and tophat2. everything started out just fine until tophat tried to search for junctions via segment mapping. I got an error 5

tophat2 -o A673_rep1_tophat2 -r 158 --mate-std-dev 44 -p 24 --microexon-search --library-type fr-unstranded --b2-sensitive --fusion-search --fusion-min-dist 50000 --fusion-multireads 5 --fusion-multipairs 5 ~/genome_reference/bowtie_indexed/hg19.bowtie2 A673_rep1_R1.fastq A673_rep1_R2.fastq 

[2012-04-11 14:16:47] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-04-11 14:16:47] Checking for Bowtie
		  Bowtie version:	 2.0.0.5
[2012-04-11 14:16:47] Checking for Samtools
		Samtools version:	 0.1.18.0
[2012-04-11 14:16:47] Checking for Bowtie index files
[2012-04-11 14:16:47] Checking for reference FASTA file
	Warning: Could not find FASTA file /Users/zehira/genome_reference/bowtie_indexed/hg19.bowtie2.fa
[2012-04-11 14:16:47] Reconstituting reference FASTA file from Bowtie index
  Executing: /Users/zehira/local/bin/bowtie2-inspect /Users/zehira/genome_reference/bowtie_indexed/hg19.bowtie2 > A673_rep1_tophat2/tmp/hg19.bowtie2.fa
[2012-04-11 14:19:57] Generating SAM header for /Users/zehira/genome_reference/bowtie_indexed/hg19.bowtie2
	format:		 fastq
	quality scale:	 phred33 (default)
[2012-04-11 14:20:00] Preparing reads
	 left reads: min. length=75, count=12942699
	right reads: min. length=75, count=12927964
[2012-04-11 14:28:54] Mapping left_kept_reads against hg19.bowtie2 with Bowtie2 
[2012-04-11 14:44:43] Mapping left_kept_reads_seg1 against hg19.bowtie2 with Bowtie2 (1/3)
[2012-04-11 14:47:28] Mapping left_kept_reads_seg2 against hg19.bowtie2 with Bowtie2 (2/3)
[2012-04-11 14:50:06] Mapping left_kept_reads_seg3 against hg19.bowtie2 with Bowtie2 (3/3)
[2012-04-11 14:53:27] Mapping right_kept_reads against hg19.bowtie2 with Bowtie2 
[2012-04-11 15:09:38] Mapping right_kept_reads_seg1 against hg19.bowtie2 with Bowtie2 (1/3)
[2012-04-11 15:12:11] Mapping right_kept_reads_seg2 against hg19.bowtie2 with Bowtie2 (2/3)
[2012-04-11 15:14:44] Mapping right_kept_reads_seg3 against hg19.bowtie2 with Bowtie2 (3/3)
[2012-04-11 15:17:26] Searching for junctions via segment mapping
	[FAILED]
Error: segment-based junction search failed with err =-5
  Reason: image not found

I'm hoping it's an easy solution and am sure it's something i did wrong. anyone has any ideas?

Thanks!