[2018-10-13 12:45:32] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:45:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:45:32] Checking for Bowtie index files (genome)..
[2018-10-13 12:45:32] Checking for reference FASTA file
[2018-10-13 12:45:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:45:36] Reading known junctions from GTF file
[2018-10-13 12:45:41] Preparing reads
	 left reads: min. length=100, max. length=100, 1423641 kept reads (109 discarded)
	right reads: min. length=100, max. length=100, 1423276 kept reads (474 discarded)
[2018-10-13 12:46:45] Building transcriptome data files /scratch/8793241.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:47:04] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:55:44] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:56:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:57:56] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:57:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:58:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:58:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:59:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:59:19] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:59:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:00:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:00:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:00:50] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:01:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:01:17] Searching for junctions via segment mapping
[2018-10-13 13:05:49] Retrieving sequences for splices
[2018-10-13 13:08:06] Indexing splices
[2018-10-13 13:08:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:08:33] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:08:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:08:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:08:53] Joining segment hits
[2018-10-13 13:11:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:11:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:11:41] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:11:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:11:54] Joining segment hits
[2018-10-13 13:14:24] Reporting output tracks
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[2018-10-13 13:23:57] A summary of the alignment counts can be found in /scratch/8793241.1.linga/tophat2/align_summary.txt
[2018-10-13 13:23:57] Run complete: 00:38:25 elapsed