[2018-10-13 14:02:01] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:02:01] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:02:01] Checking for Bowtie index files (genome)..
[2018-10-13 14:02:01] Checking for reference FASTA file
[2018-10-13 14:02:01] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:02:05] Reading known junctions from GTF file
[2018-10-13 14:02:09] Preparing reads
	 left reads: min. length=100, max. length=100, 860774 kept reads (54 discarded)
	right reads: min. length=100, max. length=100, 860563 kept reads (265 discarded)
[2018-10-13 14:02:44] Building transcriptome data files /scratch/8793278.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:03:02] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:10:44] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:11:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:12:15] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:12:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:12:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:12:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:13:00] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:13:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:13:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:13:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:13:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:14:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:14:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:14:26] Searching for junctions via segment mapping
[2018-10-13 14:18:32] Retrieving sequences for splices
[2018-10-13 14:20:30] Indexing splices
[2018-10-13 14:20:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:20:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:20:59] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:21:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:21:10] Joining segment hits
[2018-10-13 14:23:26] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:23:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:23:36] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:23:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:23:47] Joining segment hits
[2018-10-13 14:26:05] Reporting output tracks
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[2018-10-13 14:34:56] A summary of the alignment counts can be found in /scratch/8793278.1.linga/tophat2/align_summary.txt
[2018-10-13 14:34:56] Run complete: 00:32:55 elapsed