[2018-10-12 21:53:50] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:53:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:53:50] Checking for Bowtie index files (genome)..
[2018-10-12 21:53:50] Checking for reference FASTA file
[2018-10-12 21:53:50] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:53:54] Reading known junctions from GTF file
[2018-10-12 21:53:58] Preparing reads
	 left reads: min. length=100, max. length=100, 351661 kept reads (291 discarded)
	right reads: min. length=100, max. length=100, 351385 kept reads (567 discarded)
[2018-10-12 21:54:12] Building transcriptome data files /scratch/8792771.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:54:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:02:22] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:02:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:03:24] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:03:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:03:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:03:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:04:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:04:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:04:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:05:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:05:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:05:20] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:05:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:05:39] Searching for junctions via segment mapping
[2018-10-12 22:08:07] Retrieving sequences for splices
[2018-10-12 22:10:19] Indexing splices
[2018-10-12 22:10:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:10:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:10:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:10:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:10:54] Joining segment hits
[2018-10-12 22:13:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:13:14] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:13:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:13:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:13:26] Joining segment hits
[2018-10-12 22:15:58] Reporting output tracks
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[2018-10-12 22:19:02] A summary of the alignment counts can be found in /scratch/8792771.1.linga/tophat2/align_summary.txt
[2018-10-12 22:19:02] Run complete: 00:25:12 elapsed