[2018-10-13 13:10:59] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:10:59] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:10:59] Checking for Bowtie index files (genome)..
[2018-10-13 13:10:59] Checking for reference FASTA file
[2018-10-13 13:10:59] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:11:05] Reading known junctions from GTF file
[2018-10-13 13:11:11] Preparing reads
	 left reads: min. length=100, max. length=100, 589960 kept reads (22 discarded)
	right reads: min. length=100, max. length=100, 589789 kept reads (193 discarded)
[2018-10-13 13:11:46] Building transcriptome data files /scratch/8793252.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:12:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:20:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:20:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:21:31] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:21:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:21:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:22:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:22:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:22:21] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:22:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:23:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:23:14] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:23:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:23:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:23:50] Searching for junctions via segment mapping
[2018-10-13 13:27:58] Retrieving sequences for splices
[2018-10-13 13:29:59] Indexing splices
[2018-10-13 13:30:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:30:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:30:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:30:34] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:30:39] Joining segment hits
[2018-10-13 13:32:56] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:33:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:33:08] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:33:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:33:21] Joining segment hits
[2018-10-13 13:35:40] Reporting output tracks
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[2018-10-13 13:41:06] A summary of the alignment counts can be found in /scratch/8793252.1.linga/tophat2/align_summary.txt
[2018-10-13 13:41:06] Run complete: 00:30:07 elapsed