[2018-10-13 14:58:16] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:58:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:58:16] Checking for Bowtie index files (genome)..
[2018-10-13 14:58:16] Checking for reference FASTA file
[2018-10-13 14:58:16] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:58:20] Reading known junctions from GTF file
[2018-10-13 14:58:24] Preparing reads
	 left reads: min. length=100, max. length=100, 1294548 kept reads (73 discarded)
	right reads: min. length=100, max. length=100, 1293936 kept reads (685 discarded)
[2018-10-13 14:59:19] Building transcriptome data files /scratch/8793306.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:59:37] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:07:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:08:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:08:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:08:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:09:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:09:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:09:53] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:10:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:10:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:10:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:11:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:11:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:11:26] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:11:38] Searching for junctions via segment mapping
[2018-10-13 15:15:31] Retrieving sequences for splices
[2018-10-13 15:17:44] Indexing splices
[2018-10-13 15:18:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:18:10] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:18:16] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:18:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:18:27] Joining segment hits
[2018-10-13 15:20:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:20:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:21:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:21:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:21:12] Joining segment hits
[2018-10-13 15:23:33] Reporting output tracks
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[2018-10-13 15:32:13] A summary of the alignment counts can be found in /scratch/8793306.1.linga/tophat2/align_summary.txt
[2018-10-13 15:32:13] Run complete: 00:33:56 elapsed