[2018-10-13 13:09:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:09:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:09:08] Checking for Bowtie index files (genome)..
[2018-10-13 13:09:08] Checking for reference FASTA file
[2018-10-13 13:09:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:09:12] Reading known junctions from GTF file
[2018-10-13 13:09:16] Preparing reads
	 left reads: min. length=100, max. length=100, 479350 kept reads (23 discarded)
	right reads: min. length=100, max. length=100, 479208 kept reads (165 discarded)
[2018-10-13 13:09:41] Building transcriptome data files /scratch/8793250.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:10:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:18:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:18:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:19:07] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:19:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:19:28] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:19:36] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:19:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:19:54] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:20:02] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:20:22] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:20:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:20:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:20:47] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:20:56] Searching for junctions via segment mapping
[2018-10-13 13:24:18] Retrieving sequences for splices
[2018-10-13 13:26:17] Indexing splices
[2018-10-13 13:26:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:26:43] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:26:48] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:26:53] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:26:58] Joining segment hits
[2018-10-13 13:29:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:29:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:29:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:29:27] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:29:33] Joining segment hits
[2018-10-13 13:31:59] Reporting output tracks
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[2018-10-13 13:38:03] A summary of the alignment counts can be found in /scratch/8793250.1.linga/tophat2/align_summary.txt
[2018-10-13 13:38:03] Run complete: 00:28:54 elapsed