[2019-07-05 11:19:33] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-07-05 11:19:33] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:19:33] Checking for Bowtie index files (genome)..
[2019-07-05 11:19:33] Checking for reference FASTA file
[2019-07-05 11:19:33] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:19:37] Reading known junctions from GTF file
[2019-07-05 11:19:40] Preparing reads
	 left reads: min. length=150, max. length=150, 23093668 kept reads (1903 discarded)
	right reads: min. length=150, max. length=150, 23079680 kept reads (15891 discarded)
[2019-07-05 11:45:32] Building transcriptome data files /scratch/7534480.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:45:51] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:51:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:16:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:42:17] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:42:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:59:05] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:00:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:01:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:03:00] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:04:21] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:05:47] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:07:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 13:28:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 13:30:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 13:32:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 13:34:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 13:36:54] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 13:39:00] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 13:41:04] Searching for junctions via segment mapping
[2019-07-05 15:49:03] Retrieving sequences for splices
[2019-07-05 15:51:24] Indexing splices
[2019-07-05 15:52:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 15:53:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 15:55:03] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 15:56:15] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 15:57:28] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 15:58:37] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 15:59:39] Joining segment hits
[2019-07-05 16:05:11] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 16:07:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 16:09:10] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 16:11:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 16:12:49] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 16:14:26] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 16:15:55] Joining segment hits
[2019-07-05 16:22:40] Reporting output tracks
-----------------------------------------------
[2019-07-05 17:52:02] A summary of the alignment counts can be found in /scratch/7534480.1.linga/tophat2/align_summary.txt
[2019-07-05 17:52:02] Run complete: 06:32:28 elapsed