[2018-10-13 00:59:26] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:59:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:59:27] Checking for Bowtie index files (genome)..
[2018-10-13 00:59:27] Checking for reference FASTA file
[2018-10-13 00:59:27] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:59:32] Reading known junctions from GTF file
[2018-10-13 00:59:36] Preparing reads
	 left reads: min. length=100, max. length=100, 304530 kept reads (192 discarded)
	right reads: min. length=100, max. length=100, 304242 kept reads (480 discarded)
[2018-10-13 00:59:51] Building transcriptome data files /scratch/8792876.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:00:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:08:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:09:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:09:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:09:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:10:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:10:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:10:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:10:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:11:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:11:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:11:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:12:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:12:17] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:12:26] Searching for junctions via segment mapping
[2018-10-13 01:15:11] Retrieving sequences for splices
[2018-10-13 01:17:19] Indexing splices
[2018-10-13 01:17:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:17:48] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:17:53] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:17:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:18:02] Joining segment hits
[2018-10-13 01:20:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:20:24] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:20:29] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:20:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:20:39] Joining segment hits
[2018-10-13 01:23:03] Reporting output tracks
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[2018-10-13 01:26:17] A summary of the alignment counts can be found in /scratch/8792876.1.linga/tophat2/align_summary.txt
[2018-10-13 01:26:17] Run complete: 00:26:50 elapsed