[2018-10-13 10:14:27] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:14:27] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:14:28] Checking for Bowtie index files (genome)..
[2018-10-13 10:14:28] Checking for reference FASTA file
[2018-10-13 10:14:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:14:31] Reading known junctions from GTF file
[2018-10-13 10:14:35] Preparing reads
	 left reads: min. length=100, max. length=100, 1168142 kept reads (115 discarded)
	right reads: min. length=100, max. length=100, 1167901 kept reads (356 discarded)
[2018-10-13 10:15:25] Building transcriptome data files /scratch/8793168.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:15:43] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:23:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:24:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:26:04] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:26:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:26:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:27:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:27:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:27:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:27:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:28:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:28:40] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:28:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:29:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:29:26] Searching for junctions via segment mapping
[2018-10-13 10:35:41] Retrieving sequences for splices
[2018-10-13 10:37:41] Indexing splices
[2018-10-13 10:38:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:38:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:38:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:38:32] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:38:40] Joining segment hits
[2018-10-13 10:41:22] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:41:30] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:41:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:41:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:42:00] Joining segment hits
[2018-10-13 10:44:22] Reporting output tracks
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[2018-10-13 10:58:57] A summary of the alignment counts can be found in /scratch/8793168.1.linga/tophat2/align_summary.txt
[2018-10-13 10:58:57] Run complete: 00:44:30 elapsed