[2018-10-13 16:59:50] Beginning TopHat run (v2.1.1)
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[2018-10-13 16:59:50] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:59:50] Checking for Bowtie index files (genome)..
[2018-10-13 16:59:50] Checking for reference FASTA file
[2018-10-13 16:59:50] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:59:57] Reading known junctions from GTF file
[2018-10-13 17:00:05] Preparing reads
	 left reads: min. length=100, max. length=100, 198414 kept reads (80 discarded)
	right reads: min. length=100, max. length=100, 198298 kept reads (196 discarded)
[2018-10-13 17:00:20] Building transcriptome data files /scratch/8793380.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:00:55] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:12:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:12:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:12:52] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:12:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:13:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:13:18] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:13:27] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:13:35] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:13:43] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:14:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:14:11] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:14:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:14:30] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:14:40] Searching for junctions via segment mapping
[2018-10-13 17:17:24] Retrieving sequences for splices
[2018-10-13 17:20:23] Indexing splices
[2018-10-13 17:20:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:20:53] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:21:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:21:06] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:21:13] Joining segment hits
[2018-10-13 17:24:16] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:24:21] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:24:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:24:33] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:24:40] Joining segment hits
[2018-10-13 17:28:23] Reporting output tracks
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[2018-10-13 17:31:42] A summary of the alignment counts can be found in /scratch/8793380.1.linga/tophat2/align_summary.txt
[2018-10-13 17:31:42] Run complete: 00:31:52 elapsed