[2018-10-12 23:03:34] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:03:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:03:34] Checking for Bowtie index files (genome)..
[2018-10-12 23:03:34] Checking for reference FASTA file
[2018-10-12 23:03:34] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:03:39] Reading known junctions from GTF file
[2018-10-12 23:03:43] Preparing reads
	 left reads: min. length=100, max. length=100, 214678 kept reads (199 discarded)
	right reads: min. length=100, max. length=100, 214472 kept reads (405 discarded)
[2018-10-12 23:03:53] Building transcriptome data files /scratch/8792818.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:04:14] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:12:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:13:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:13:34] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:13:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:14:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:14:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:14:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:14:35] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:14:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:15:15] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:15:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:15:36] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:15:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:15:55] Searching for junctions via segment mapping
[2018-10-12 23:18:25] Retrieving sequences for splices
[2018-10-12 23:20:36] Indexing splices
[2018-10-12 23:20:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:21:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:21:07] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:21:11] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:21:15] Joining segment hits
[2018-10-12 23:23:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:23:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:23:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:23:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:23:49] Joining segment hits
[2018-10-12 23:26:07] Reporting output tracks
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[2018-10-12 23:29:14] A summary of the alignment counts can be found in /scratch/8792818.1.linga/tophat2/align_summary.txt
[2018-10-12 23:29:14] Run complete: 00:25:40 elapsed