Tophat2: Not getting an accepted_hits.bam output

[rndouglas]

I am having some trouble with Tophat2/Bowtie2.

I ran the following:

tophat2 -p 4 -o ~/B73B2 -i 60 -I 4000 -G ~/gDNA.gtf ~/bowtie2_files/MaizeGDNA_B ~/B73B2.fastq

Everything seems to run well:

[2012-10-30 22:17:48] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-10-30 22:17:48] Checking for Bowtie
                  Bowtie version:        2.0.0.7
[2012-10-30 22:17:48] Checking for Samtools
                Samtools version:        0.1.18.0
[2012-10-30 22:17:48] Checking for Bowtie index files
[2012-10-30 22:17:48] Checking for reference FASTA file
[2012-10-30 22:17:48] Generating SAM header for /home/rdouglas/data/bowtie_files/MaizeGDNA_B
        format:          fastq
        quality scale:   phred33 (default)
[2012-10-30 22:18:12] Reading known junctions from GTF file
[2012-10-30 22:18:19] Preparing reads
         left reads: min. length=100, max. length=100, 64796485 kept reads (110651 discarded)
[2012-10-30 22:42:11] Creating transcriptome data files..
[2012-10-30 22:42:53] Building Bowtie index from MaizeGDNA_B.fa
[2012-10-30 22:52:35] Mapping left_kept_reads to transcriptome MaizeGDNA_B with Bowtie2
[2012-10-30 23:35:53] Resuming TopHat pipeline with unmapped reads
[2012-10-30 23:35:53] Mapping left_kept_reads.m2g_um to genome MaizeGDNA_B with Bowtie2
[2012-10-31 09:48:42] Mapping left_kept_reads.m2g_um_seg1 to genome MaizeGDNA_B with Bowtie2 (1/4)
[2012-10-31 11:30:34] Mapping left_kept_reads.m2g_um_seg2 to genome MaizeGDNA_B with Bowtie2 (2/4)
[2012-10-31 13:12:53] Mapping left_kept_reads.m2g_um_seg3 to genome MaizeGDNA_B with Bowtie2 (3/4)
[2012-10-31 14:51:47] Mapping left_kept_reads.m2g_um_seg4 to genome MaizeGDNA_B with Bowtie2 (4/4)
[2012-10-31 15:54:52] Searching for junctions via segment mapping
[2012-10-31 16:33:49] Retrieving sequences for splices
[2012-10-31 16:35:22] Indexing splices
[2012-10-31 16:36:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2012-10-31 17:19:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2012-10-31 18:13:30] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2012-10-31 18:49:04] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2012-10-31 19:01:19] Joining segment hits
[2012-11-01 01:37:12] Reporting output tracks
-----------------------------------------------
[2012-11-01 03:49:39] Run complete: 1 days 05:31:50 elapsed

Except the only output files I get at the end are: deletions.bed, insertions.bed, junctions.bed, log folder, prep_reads.info, and unmapped.bam.

I previously ran the same FASTQ/GTF with Tophat/Bowtie and had millions of mapped reads. Now I'm 0-for-2 with Tophat2.

Does anyone have any suggestions that might help recover an accepted_hits.bam file (other than going back to Tophat/Bowtie)?

[jp.]

Hi rndouglas
did you get solution ?
My tophat run gives me no error and no accepted_hits.bam...I have 30GB mem ....???

[dpryan]

Hi rndouglas
did you get solution ?
My tophat run gives me no error and no accepted_hits.bam...I have 30GB mem ....???

Did you check any of the logs that tophat creates?

[jp.]

I have checked logs but dont know what to find. However, log says that .bam file was generated in wd but is not there ????