[2018-10-13 18:03:21] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:03:21] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:03:21] Checking for Bowtie index files (genome)..
[2018-10-13 18:03:21] Checking for reference FASTA file
[2018-10-13 18:03:21] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:03:25] Reading known junctions from GTF file
[2018-10-13 18:03:30] Preparing reads
	 left reads: min. length=100, max. length=100, 237028 kept reads (144 discarded)
	right reads: min. length=100, max. length=100, 236742 kept reads (430 discarded)
[2018-10-13 18:03:41] Building transcriptome data files /scratch/8793424.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:04:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:12:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:12:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:13:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:13:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:13:32] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:13:40] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:13:50] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:13:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:14:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:14:33] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:14:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:14:52] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:15:01] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:15:10] Searching for junctions via segment mapping
[2018-10-13 18:17:43] Retrieving sequences for splices
[2018-10-13 18:19:54] Indexing splices
[2018-10-13 18:20:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:20:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:20:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:20:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:20:30] Joining segment hits
[2018-10-13 18:22:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:22:43] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:22:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:22:52] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:22:56] Joining segment hits
[2018-10-13 18:25:14] Reporting output tracks
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[2018-10-13 18:27:58] A summary of the alignment counts can be found in /scratch/8793424.1.linga/tophat2/align_summary.txt
[2018-10-13 18:27:58] Run complete: 00:24:36 elapsed