[2018-10-13 18:28:11] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:28:11] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:28:11] Checking for Bowtie index files (genome)..
[2018-10-13 18:28:11] Checking for reference FASTA file
[2018-10-13 18:28:11] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:28:16] Reading known junctions from GTF file
[2018-10-13 18:28:20] Preparing reads
	 left reads: min. length=100, max. length=100, 560918 kept reads (336 discarded)
	right reads: min. length=100, max. length=100, 560432 kept reads (822 discarded)
[2018-10-13 18:28:46] Building transcriptome data files /scratch/8793439.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:29:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:37:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:38:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:38:41] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:38:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:39:18] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:39:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:39:43] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:39:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:40:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:40:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:40:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:41:10] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:41:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:41:34] Searching for junctions via segment mapping
[2018-10-13 18:44:31] Retrieving sequences for splices
[2018-10-13 18:46:32] Indexing splices
[2018-10-13 18:46:51] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:46:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:47:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:47:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:47:09] Joining segment hits
[2018-10-13 18:49:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:49:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:49:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:49:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:49:49] Joining segment hits
[2018-10-13 18:52:05] Reporting output tracks
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[2018-10-13 18:55:44] A summary of the alignment counts can be found in /scratch/8793439.1.linga/tophat2/align_summary.txt
[2018-10-13 18:55:44] Run complete: 00:27:33 elapsed