[2018-10-13 09:00:14] Beginning TopHat run (v2.1.1)
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[2018-10-13 09:00:14] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:00:14] Checking for Bowtie index files (genome)..
[2018-10-13 09:00:14] Checking for reference FASTA file
[2018-10-13 09:00:14] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:00:18] Reading known junctions from GTF file
[2018-10-13 09:00:22] Preparing reads
	 left reads: min. length=100, max. length=100, 1315831 kept reads (152 discarded)
	right reads: min. length=100, max. length=100, 1315529 kept reads (454 discarded)
[2018-10-13 09:01:22] Building transcriptome data files /scratch/8793132.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:01:43] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:10:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:11:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:13:41] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:13:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:14:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:14:42] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:15:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:15:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:15:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:16:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:16:35] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:16:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:17:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:17:28] Searching for junctions via segment mapping
[2018-10-13 09:25:55] Retrieving sequences for splices
[2018-10-13 09:28:07] Indexing splices
[2018-10-13 09:28:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:28:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:28:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:29:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:29:20] Joining segment hits
[2018-10-13 09:31:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:31:59] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:32:13] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:32:25] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:32:35] Joining segment hits
[2018-10-13 09:35:10] Reporting output tracks
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[2018-10-13 09:59:18] A summary of the alignment counts can be found in /scratch/8793132.1.linga/tophat2/align_summary.txt
[2018-10-13 09:59:18] Run complete: 00:59:04 elapsed