[2018-10-13 08:06:07] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:06:07] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:06:07] Checking for Bowtie index files (genome)..
[2018-10-13 08:06:07] Checking for reference FASTA file
[2018-10-13 08:06:07] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:06:11] Reading known junctions from GTF file
[2018-10-13 08:06:15] Preparing reads
	 left reads: min. length=100, max. length=100, 892394 kept reads (81 discarded)
	right reads: min. length=100, max. length=100, 892105 kept reads (370 discarded)
[2018-10-13 08:06:49] Building transcriptome data files /scratch/8793106.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:07:06] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:15:13] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:15:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:16:35] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:16:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:17:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:17:20] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:17:33] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:17:43] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:17:53] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:18:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:18:32] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:18:44] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:18:54] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:19:05] Searching for junctions via segment mapping
[2018-10-13 08:22:37] Retrieving sequences for splices
[2018-10-13 08:24:45] Indexing splices
[2018-10-13 08:25:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:25:11] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:25:17] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:25:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:25:26] Joining segment hits
[2018-10-13 08:27:55] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:27:59] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:28:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:28:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:28:14] Joining segment hits
[2018-10-13 08:30:48] Reporting output tracks
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[2018-10-13 08:36:16] A summary of the alignment counts can be found in /scratch/8793106.1.linga/tophat2/align_summary.txt
[2018-10-13 08:36:16] Run complete: 00:30:09 elapsed