[2019-07-05 11:19:08] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-05 11:19:08] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:19:08] Checking for Bowtie index files (genome)..
[2019-07-05 11:19:08] Checking for reference FASTA file
[2019-07-05 11:19:08] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:19:13] Reading known junctions from GTF file
[2019-07-05 11:19:16] Preparing reads
	 left reads: min. length=150, max. length=150, 24464217 kept reads (1938 discarded)
	right reads: min. length=150, max. length=150, 24449181 kept reads (16974 discarded)
[2019-07-05 11:45:45] Building transcriptome data files /scratch/7534475.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:46:02] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:52:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:19:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:47:21] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:47:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:06:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:07:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:09:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:10:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:12:31] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:14:09] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:15:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:37:55] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:40:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:43:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:45:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:48:33] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:51:08] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:53:31] Searching for junctions via segment mapping
[2019-07-05 16:05:03] Retrieving sequences for splices
[2019-07-05 16:07:26] Indexing splices
[2019-07-05 16:09:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:10:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:11:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:13:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:14:49] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:16:06] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:17:10] Joining segment hits
[2019-07-05 16:22:45] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:24:42] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:26:49] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:28:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:30:46] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:32:39] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:34:20] Joining segment hits
[2019-07-05 16:41:26] Reporting output tracks
-----------------------------------------------
[2019-07-05 18:17:30] A summary of the alignment counts can be found in /scratch/7534475.1.linga/tophat2/align_summary.txt
[2019-07-05 18:17:30] Run complete: 06:58:22 elapsed