[2018-10-13 11:51:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:51:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:51:03] Checking for Bowtie index files (genome)..
[2018-10-13 11:51:03] Checking for reference FASTA file
[2018-10-13 11:51:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:51:08] Reading known junctions from GTF file
[2018-10-13 11:51:12] Preparing reads
	 left reads: min. length=100, max. length=100, 538617 kept reads (47 discarded)
	right reads: min. length=100, max. length=100, 538516 kept reads (148 discarded)
[2018-10-13 11:51:39] Building transcriptome data files /scratch/8793219.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:51:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:00:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:00:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:01:20] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:01:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:01:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:01:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:02:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:02:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:02:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:02:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:02:43] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:02:53] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:03:02] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:03:11] Searching for junctions via segment mapping
[2018-10-13 12:06:37] Retrieving sequences for splices
[2018-10-13 12:08:39] Indexing splices
[2018-10-13 12:08:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:09:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:09:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:09:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:09:17] Joining segment hits
[2018-10-13 12:11:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:11:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:11:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:11:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:11:54] Joining segment hits
[2018-10-13 12:14:17] Reporting output tracks
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[2018-10-13 12:19:47] A summary of the alignment counts can be found in /scratch/8793219.1.linga/tophat2/align_summary.txt
[2018-10-13 12:19:47] Run complete: 00:28:43 elapsed