[2018-10-12 21:10:14] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:10:14] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:10:14] Checking for Bowtie index files (genome)..
[2018-10-12 21:10:14] Checking for reference FASTA file
[2018-10-12 21:10:14] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:10:20] Reading known junctions from GTF file
[2018-10-12 21:10:25] Preparing reads
	 left reads: min. length=100, max. length=100, 295471 kept reads (223 discarded)
	right reads: min. length=100, max. length=100, 295191 kept reads (503 discarded)
[2018-10-12 21:10:40] Building transcriptome data files /scratch/8792747.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:11:01] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:19:42] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:20:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:20:49] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:20:49] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:21:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:21:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:21:47] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:21:58] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:22:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:22:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:22:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:23:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:23:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:23:29] Searching for junctions via segment mapping
[2018-10-12 21:26:12] Retrieving sequences for splices
[2018-10-12 21:28:30] Indexing splices
[2018-10-12 21:28:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:28:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:29:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:29:04] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:29:08] Joining segment hits
[2018-10-12 21:31:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:31:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:31:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:31:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:31:59] Joining segment hits
[2018-10-12 21:34:32] Reporting output tracks
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[2018-10-12 21:37:53] A summary of the alignment counts can be found in /scratch/8792747.1.linga/tophat2/align_summary.txt
[2018-10-12 21:37:53] Run complete: 00:27:38 elapsed