[2018-10-12 22:04:22] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:04:22] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:04:22] Checking for Bowtie index files (genome)..
[2018-10-12 22:04:22] Checking for reference FASTA file
[2018-10-12 22:04:22] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:04:26] Reading known junctions from GTF file
[2018-10-12 22:04:30] Preparing reads
	 left reads: min. length=100, max. length=100, 384658 kept reads (210 discarded)
	right reads: min. length=100, max. length=100, 384394 kept reads (474 discarded)
[2018-10-12 22:04:48] Building transcriptome data files /scratch/8792781.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:05:08] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:13:10] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:13:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:14:20] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:14:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:15:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:15:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:15:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:15:31] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:15:41] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:16:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:16:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:16:43] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:16:53] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:17:03] Searching for junctions via segment mapping
[2018-10-12 22:19:37] Retrieving sequences for splices
[2018-10-12 22:21:38] Indexing splices
[2018-10-12 22:21:57] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:22:01] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:22:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:22:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:22:14] Joining segment hits
[2018-10-12 22:24:49] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:24:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:24:58] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:25:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:25:06] Joining segment hits
[2018-10-12 22:27:12] Reporting output tracks
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[2018-10-12 22:30:21] A summary of the alignment counts can be found in /scratch/8792781.1.linga/tophat2/align_summary.txt
[2018-10-12 22:30:21] Run complete: 00:25:59 elapsed