[2018-10-13 13:10:58] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:10:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:10:58] Checking for Bowtie index files (genome)..
[2018-10-13 13:10:58] Checking for reference FASTA file
[2018-10-13 13:10:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:11:02] Reading known junctions from GTF file
[2018-10-13 13:11:07] Preparing reads
	 left reads: min. length=100, max. length=100, 1062637 kept reads (89 discarded)
	right reads: min. length=100, max. length=100, 1062453 kept reads (273 discarded)
[2018-10-13 13:11:52] Building transcriptome data files /scratch/8793253.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:12:11] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:19:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:20:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:21:41] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:21:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:22:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:22:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:22:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:22:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:23:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:23:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:23:58] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:24:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:24:25] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:24:36] Searching for junctions via segment mapping
[2018-10-13 13:27:57] Retrieving sequences for splices
[2018-10-13 13:30:06] Indexing splices
[2018-10-13 13:30:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:30:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:30:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:30:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:30:46] Joining segment hits
[2018-10-13 13:33:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:33:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:33:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:33:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:33:37] Joining segment hits
[2018-10-13 13:35:56] Reporting output tracks
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[2018-10-13 13:42:04] A summary of the alignment counts can be found in /scratch/8793253.1.linga/tophat2/align_summary.txt
[2018-10-13 13:42:04] Run complete: 00:31:06 elapsed