Tophat2: Error running bowtie:

[Nextgenanalysis]

Thanks,
but I solved it. Ran out of memory...

can you please tell what is your system configuration and which genome are you using

[GenoMax]

Hi dfhdfh:

I am newer in NGS analysis. I recently used tophat2 to align illumina PE RNA-seq. At the end of running, there is an error, I really don't know how to solve this problem. Please help, thanks.
I am using Oracle VM VirtualBox linux system.

calgary@ChanLab:~/BT2_HOME$ tophat2 -o 81MAGABXX_5PE ./indexes/hg19 /media/sf_F_DRIVE/finished/81MAGABXX_5_R1.fastq /media/sf_F_DRIVE/finished/81MAGABXX_5_R2.fastq

[2013-04-26 15:28:53] Beginning TopHat run (v2.0.8)

[2013-04-28 19:39:27] Reporting output tracks
[FAILED]
Error: [Errno 2] No such file or directory
Found 313015 junctions from happy spliced reads

Ouch. It is painful to get that error after running the analysis for 2 days!

So it did not make the "81MAGABXX_5PE" directory?

[chanwu]

Tophat2 error at the end

Hi dfhdfh:

I am newer in NGS analysis. I recently used tophat2 to align illumina PE RNA-seq. At the end of running, there is an error, I really don't know how to solve this problem. Please help, thanks.
I am using Oracle VM VirtualBox linux system.

calgary@ChanLab:~/BT2_HOME$ tophat2 -o 81MAGABXX_5PE ./indexes/hg19 /media/sf_F_DRIVE/finished/81MAGABXX_5_R1.fastq /media/sf_F_DRIVE/finished/81MAGABXX_5_R2.fastq

[2013-04-26 15:28:53] Beginning TopHat run (v2.0.8)
-----------------------------------------------
[2013-04-26 15:28:53] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-04-26 15:28:53] Checking for Samtools
Samtools version: 0.1.18.0
[2013-04-26 15:28:53] Checking for Bowtie index files
[2013-04-26 15:28:53] Checking for reference FASTA file
[2013-04-26 15:28:53] Generating SAM header for ./indexes/hg19
format: fastq
quality scale: phred33 (default)
[2013-04-26 15:29:26] 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)
[2013-04-26 16:17:30] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-04-27 07:09:46] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4)
[2013-04-27 08:22:55] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 (2/4)
[2013-04-27 09:35:45] Mapping left_kept_reads_seg3 to genome hg19 with Bowtie2 (3/4)
[2013-04-27 10:57:53] Mapping left_kept_reads_seg4 to genome hg19 with Bowtie2 (4/4)
[2013-04-27 12:17:29] Mapping right_kept_reads to genome hg19 with Bowtie2
[2013-04-28 07:23:39] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 (1/4)
[2013-04-28 08:35:06] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 (2/4)
[2013-04-28 09:44:22] Mapping right_kept_reads_seg3 to genome hg19 with Bowtie2 (3/4)
[2013-04-28 11:43:32] Mapping right_kept_reads_seg4 to genome hg19 with Bowtie2 (4/4)
[2013-04-28 13:01:44] Searching for junctions via segment mapping
[2013-04-28 15:05:19] Retrieving sequences for splices
[2013-04-28 15:07:08] Indexing splices
[2013-04-28 15:09:25] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2013-04-28 15:33:00] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2013-04-28 15:56:47] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2013-04-28 16:21:29] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2013-04-28 16:43:47] Joining segment hits
[2013-04-28 17:22:01] Mapping right_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2013-04-28 17:44:55] Mapping right_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2013-04-28 18:06:19] Mapping right_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2013-04-28 18:33:27] Mapping right_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2013-04-28 18:53:58] Joining segment hits
[2013-04-28 19:39:27] Reporting output tracks
[FAILED]
Error: [Errno 2] No such file or directory
Found 313015 junctions from happy spliced reads

I am trying to map illumina paired-end datasets using tophat2. Everything seems to work fine but I suddenly get an errormessage concerning bowtie:

[2013-02-15 16:16:36] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-15 16:16:36] Checking for Bowtie
Bowtie version: 2.0.6.0
[2013-02-15 16:16:36] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-15 16:16:36] Checking for Bowtie index files
[2013-02-15 16:16:36] Checking for reference FASTA file
[2013-02-15 16:16:36] Generating SAM header for /usit/abel/u1/jonbra/Sycon-diff-expr-test/sycon_genome
format: fastq
quality scale: phred33 (default)
[2013-02-15 16:16:42] Preparing reads
left reads: min. length=101, max. length=101, 20383888 kept reads (10376 discarded)
[2013-02-15 16:23:29] Mapping left_kept_reads to genome sycon_genome with Bowtie2
[FAILED]
Error running bowtie:

[JonB]

Thanks,
but I solved it. Ran out of memory...

[dfhdfh]

Please look at the tophat.log file. Does it give you an error?

[JonB]

I am trying to map illumina paired-end datasets using tophat2. Everything seems to work fine but I suddenly get an errormessage concerning bowtie:

[2013-02-15 16:16:36] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-15 16:16:36] Checking for Bowtie
Bowtie version: 2.0.6.0
[2013-02-15 16:16:36] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-15 16:16:36] Checking for Bowtie index files
[2013-02-15 16:16:36] Checking for reference FASTA file
[2013-02-15 16:16:36] Generating SAM header for /usit/abel/u1/jonbra/Sycon-diff-expr-test/sycon_genome
format: fastq
quality scale: phred33 (default)
[2013-02-15 16:16:42] Preparing reads
left reads: min. length=101, max. length=101, 20383888 kept reads (10376 discarded)
[2013-02-15 16:23:29] Mapping left_kept_reads to genome sycon_genome with Bowtie2
[FAILED]
Error running bowtie: