Hello All,
I'm doing Tophat2 on 10 samples, from which 3 samples should contain RNA-seq spikes sequences. I've build my own index files from +- 8 spike sequences via bowtie2-build. Now i'm trying to use Tophat2 whether to check if the spike sequences are found in the samples or not. Everything works fine untill I get one error I can't fix:
Anyone knows whats going wrong?
I'm doing Tophat2 on 10 samples, from which 3 samples should contain RNA-seq spikes sequences. I've build my own index files from +- 8 spike sequences via bowtie2-build. Now i'm trying to use Tophat2 whether to check if the spike sequences are found in the samples or not. Everything works fine untill I get one error I can't fix:
Code:
[2014-02-19 09:06:01] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2014-02-19 09:06:01] Checking for Bowtie Bowtie version: 2.1.0.0 [2014-02-19 09:06:01] Checking for Samtools Samtools version: 0.1.19.0 [2014-02-19 09:06:01] Checking for Bowtie index files (genome).. [2014-02-19 09:06:01] Checking for reference FASTA file [2014-02-19 09:06:01] Generating SAM header for /indexes_spikes/spikes format: fastq quality scale: phred33 (default) [2014-02-19 09:06:02] Preparing reads left reads: min. length=139, max. length=151, 424139 kept reads (30263 discarded) [2014-02-19 09:06:19] Mapping left_kept_reads to genome spikes with Bowtie2 [2014-02-19 09:09:37] Mapping left_kept_reads_seg1 to genome spikes with Bowtie2 (1/6) [2014-02-19 09:09:54] Mapping left_kept_reads_seg2 to genome spikes with Bowtie2 (2/6) [2014-02-19 09:10:12] Mapping left_kept_reads_seg3 to genome spikes with Bowtie2 (3/6) [2014-02-19 09:10:28] Mapping left_kept_reads_seg4 to genome spikes with Bowtie2 (4/6) [2014-02-19 09:10:44] Mapping left_kept_reads_seg5 to genome spikes with Bowtie2 (5/6) [2014-02-19 09:10:58] Mapping left_kept_reads_seg6 to genome spikes with Bowtie2 (6/6) [2014-02-19 09:11:11] Searching for junctions via segment mapping Warning: junction database is empty! [2014-02-19 09:12:10] Reporting output tracks [FAILED]
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