[2018-10-13 16:56:32] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:56:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:56:32] Checking for Bowtie index files (genome)..
[2018-10-13 16:56:32] Checking for reference FASTA file
[2018-10-13 16:56:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:56:37] Reading known junctions from GTF file
[2018-10-13 16:56:43] Preparing reads
	 left reads: min. length=100, max. length=100, 229375 kept reads (209 discarded)
	right reads: min. length=100, max. length=100, 229188 kept reads (396 discarded)
[2018-10-13 16:56:53] Building transcriptome data files /scratch/8793376.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:57:14] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:05:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:06:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:06:29] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:06:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:06:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:06:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:07:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:07:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:07:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:07:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:07:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:08:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:08:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:08:21] Searching for junctions via segment mapping
[2018-10-13 17:11:00] Retrieving sequences for splices
[2018-10-13 17:13:11] Indexing splices
[2018-10-13 17:13:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:13:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:13:40] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:13:44] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:13:48] Joining segment hits
[2018-10-13 17:16:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:17:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:17:06] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:17:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:17:15] Joining segment hits
[2018-10-13 17:19:27] Reporting output tracks
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[2018-10-13 17:22:27] A summary of the alignment counts can be found in /scratch/8793376.1.linga/tophat2/align_summary.txt
[2018-10-13 17:22:27] Run complete: 00:25:54 elapsed