[2018-10-13 00:19:37] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 00:19:37] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:19:37] Checking for Bowtie index files (genome)..
[2018-10-13 00:19:37] Checking for reference FASTA file
[2018-10-13 00:19:37] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:19:42] Reading known junctions from GTF file
[2018-10-13 00:19:47] Preparing reads
	 left reads: min. length=100, max. length=100, 522294 kept reads (263 discarded)
	right reads: min. length=100, max. length=100, 521806 kept reads (751 discarded)
[2018-10-13 00:20:09] Building transcriptome data files /scratch/8792862.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:20:30] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:29:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:30:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:31:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:31:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:32:07] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:32:20] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:32:42] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:32:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:33:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:34:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:34:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:34:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:34:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:35:03] Searching for junctions via segment mapping
[2018-10-13 00:38:04] Retrieving sequences for splices
[2018-10-13 00:40:23] Indexing splices
[2018-10-13 00:40:45] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:40:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:40:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:40:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:41:03] Joining segment hits
[2018-10-13 00:43:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:43:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:43:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:43:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:43:50] Joining segment hits
[2018-10-13 00:46:59] Reporting output tracks
-----------------------------------------------
[2018-10-13 00:51:01] A summary of the alignment counts can be found in /scratch/8792862.1.linga/tophat2/align_summary.txt
[2018-10-13 00:51:01] Run complete: 00:31:23 elapsed