[2018-10-12 21:08:41] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:08:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:08:41] Checking for Bowtie index files (genome)..
[2018-10-12 21:08:41] Checking for reference FASTA file
[2018-10-12 21:08:41] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:08:46] Reading known junctions from GTF file
[2018-10-12 21:08:51] Preparing reads
	 left reads: min. length=100, max. length=100, 268412 kept reads (157 discarded)
	right reads: min. length=100, max. length=100, 268197 kept reads (372 discarded)
[2018-10-12 21:09:03] Building transcriptome data files /scratch/8792746.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:09:23] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:17:50] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:18:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:18:44] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:18:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:19:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:19:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:19:37] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:19:46] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:19:56] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:20:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:20:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:20:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:20:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:21:08] Searching for junctions via segment mapping
[2018-10-12 21:23:38] Retrieving sequences for splices
[2018-10-12 21:25:42] Indexing splices
[2018-10-12 21:26:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:26:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:26:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:26:13] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:26:17] Joining segment hits
[2018-10-12 21:28:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:28:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:28:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:28:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:28:57] Joining segment hits
[2018-10-12 21:31:17] Reporting output tracks
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[2018-10-12 21:34:18] A summary of the alignment counts can be found in /scratch/8792746.1.linga/tophat2/align_summary.txt
[2018-10-12 21:34:18] Run complete: 00:25:36 elapsed