[2018-10-13 15:18:29] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 15:18:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:18:29] Checking for Bowtie index files (genome)..
[2018-10-13 15:18:29] Checking for reference FASTA file
[2018-10-13 15:18:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:18:34] Reading known junctions from GTF file
[2018-10-13 15:18:38] Preparing reads
	 left reads: min. length=100, max. length=100, 1124069 kept reads (63 discarded)
	right reads: min. length=100, max. length=100, 1123840 kept reads (292 discarded)
[2018-10-13 15:19:24] Building transcriptome data files /scratch/8793314.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:19:44] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:28:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:28:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:29:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:29:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:30:17] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:30:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:30:39] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:30:50] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:31:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:31:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:31:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:31:57] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:32:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:32:20] Searching for junctions via segment mapping
[2018-10-13 15:36:06] Retrieving sequences for splices
[2018-10-13 15:38:12] Indexing splices
[2018-10-13 15:38:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:38:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:38:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:38:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:38:57] Joining segment hits
[2018-10-13 15:41:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:41:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:41:41] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:41:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:41:51] Joining segment hits
[2018-10-13 15:44:14] Reporting output tracks
-----------------------------------------------
[2018-10-13 15:51:58] A summary of the alignment counts can be found in /scratch/8793314.1.linga/tophat2/align_summary.txt
[2018-10-13 15:51:58] Run complete: 00:33:28 elapsed