[2018-10-13 06:08:42] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:08:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:08:43] Checking for Bowtie index files (genome)..
[2018-10-13 06:08:43] Checking for reference FASTA file
[2018-10-13 06:08:43] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:08:47] Reading known junctions from GTF file
[2018-10-13 06:08:53] Preparing reads
	 left reads: min. length=100, max. length=100, 1458313 kept reads (90 discarded)
	right reads: min. length=100, max. length=100, 1457914 kept reads (489 discarded)
[2018-10-13 06:10:03] Building transcriptome data files /scratch/8793046.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:10:24] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:19:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:20:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:22:01] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:22:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:23:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:23:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:23:45] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:23:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:24:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:25:01] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:25:14] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:25:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:25:48] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:26:02] Searching for junctions via segment mapping
[2018-10-13 06:31:02] Retrieving sequences for splices
[2018-10-13 06:33:13] Indexing splices
[2018-10-13 06:33:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:33:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:33:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:33:57] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:34:03] Joining segment hits
[2018-10-13 06:36:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:36:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:36:53] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:37:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:37:06] Joining segment hits
[2018-10-13 06:39:40] Reporting output tracks
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[2018-10-13 06:51:22] A summary of the alignment counts can be found in /scratch/8793046.1.linga/tophat2/align_summary.txt
[2018-10-13 06:51:22] Run complete: 00:42:39 elapsed