[2018-10-12 22:01:58] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:01:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:01:58] Checking for Bowtie index files (genome)..
[2018-10-12 22:01:58] Checking for reference FASTA file
[2018-10-12 22:01:58] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:02:02] Reading known junctions from GTF file
[2018-10-12 22:02:07] Preparing reads
	 left reads: min. length=100, max. length=100, 415488 kept reads (306 discarded)
	right reads: min. length=100, max. length=100, 415111 kept reads (683 discarded)
[2018-10-12 22:02:26] Building transcriptome data files /scratch/8792778.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:02:47] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:11:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:12:44] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:13:34] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:13:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:14:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:14:37] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:14:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:15:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:15:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:16:08] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:16:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:16:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:16:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:16:57] Searching for junctions via segment mapping
[2018-10-12 22:19:44] Retrieving sequences for splices
[2018-10-12 22:21:58] Indexing splices
[2018-10-12 22:22:21] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:22:26] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:22:31] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:22:36] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:22:40] Joining segment hits
[2018-10-12 22:25:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:25:07] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:25:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:25:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:25:21] Joining segment hits
[2018-10-12 22:27:54] Reporting output tracks
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[2018-10-12 22:31:35] A summary of the alignment counts can be found in /scratch/8792778.1.linga/tophat2/align_summary.txt
[2018-10-12 22:31:35] Run complete: 00:29:36 elapsed