[2017-06-16 10:19:49] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2017-06-16 10:19:49] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:19:49] Checking for Bowtie index files (genome)..
[2017-06-16 10:19:49] Checking for reference FASTA file
[2017-06-16 10:19:49] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:19:53] Reading known junctions from GTF file
[2017-06-16 10:19:55] Preparing reads
	 left reads: min. length=101, max. length=101, 20706772 kept reads (4971 discarded)
	right reads: min. length=101, max. length=101, 20693823 kept reads (17920 discarded)
[2017-06-16 10:39:19] Building transcriptome data files /scratch/9351455.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 10:39:37] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 10:41:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:55:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 11:08:54] Resuming TopHat pipeline with unmapped reads
[2017-06-16 11:08:54] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:23:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:25:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:27:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:29:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:32:00] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:45:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:47:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:50:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:52:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:55:17] Searching for junctions via segment mapping
[2017-06-16 12:12:16] Retrieving sequences for splices
[2017-06-16 12:15:03] Indexing splices
[2017-06-16 12:15:54] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:17:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:18:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:19:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:20:50] Joining segment hits
[2017-06-16 12:24:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:26:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:27:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:28:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:29:53] Joining segment hits
[2017-06-16 12:34:12] Reporting output tracks
-----------------------------------------------
[2017-06-16 13:02:29] A summary of the alignment counts can be found in /scratch/9351455.1.linga/tophat2/align_summary.txt
[2017-06-16 13:02:29] Run complete: 02:42:40 elapsed