[2018-10-13 11:46:28] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:46:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:46:28] Checking for Bowtie index files (genome)..
[2018-10-13 11:46:28] Checking for reference FASTA file
[2018-10-13 11:46:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:46:32] Reading known junctions from GTF file
[2018-10-13 11:46:37] Preparing reads
	 left reads: min. length=100, max. length=100, 1139164 kept reads (73 discarded)
	right reads: min. length=100, max. length=100, 1138967 kept reads (270 discarded)
[2018-10-13 11:47:25] Building transcriptome data files /scratch/8793214.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:47:44] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:55:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:57:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:00:12] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:00:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:01:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:01:14] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:01:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:01:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:02:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:02:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:03:02] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:03:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:03:42] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:03:58] Searching for junctions via segment mapping
[2018-10-13 12:13:19] Retrieving sequences for splices
[2018-10-13 12:15:31] Indexing splices
[2018-10-13 12:16:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:16:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:16:28] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:16:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:16:54] Joining segment hits
[2018-10-13 12:19:30] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:19:40] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:19:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:20:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:20:19] Joining segment hits
[2018-10-13 12:22:58] Reporting output tracks
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[2018-10-13 12:51:56] A summary of the alignment counts can be found in /scratch/8793214.1.linga/tophat2/align_summary.txt
[2018-10-13 12:51:56] Run complete: 01:05:28 elapsed