[2018-10-13 08:15:32] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 08:15:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:15:32] Checking for Bowtie index files (genome)..
[2018-10-13 08:15:32] Checking for reference FASTA file
[2018-10-13 08:15:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:15:37] Reading known junctions from GTF file
[2018-10-13 08:15:42] Preparing reads
	 left reads: min. length=100, max. length=100, 1310718 kept reads (90 discarded)
	right reads: min. length=100, max. length=100, 1310236 kept reads (572 discarded)
[2018-10-13 08:16:43] Building transcriptome data files /scratch/8793109.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:17:05] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:25:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:26:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:28:17] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:28:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:28:56] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:29:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:29:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:29:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:29:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:30:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:30:38] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:30:53] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:31:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:31:18] Searching for junctions via segment mapping
[2018-10-13 08:36:24] Retrieving sequences for splices
[2018-10-13 08:38:34] Indexing splices
[2018-10-13 08:38:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:39:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:39:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:39:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:39:29] Joining segment hits
[2018-10-13 08:42:00] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:42:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:42:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:42:23] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:42:31] Joining segment hits
[2018-10-13 08:45:02] Reporting output tracks
-----------------------------------------------
[2018-10-13 09:01:28] A summary of the alignment counts can be found in /scratch/8793109.1.linga/tophat2/align_summary.txt
[2018-10-13 09:01:28] Run complete: 00:45:55 elapsed