[2018-10-13 05:55:20] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:55:20] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:55:20] Checking for Bowtie index files (genome)..
[2018-10-13 05:55:20] Checking for reference FASTA file
[2018-10-13 05:55:20] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:55:25] Reading known junctions from GTF file
[2018-10-13 05:55:30] Preparing reads
	 left reads: min. length=100, max. length=100, 1135899 kept reads (285 discarded)
	right reads: min. length=100, max. length=100, 1135581 kept reads (603 discarded)
[2018-10-13 05:56:16] Building transcriptome data files /scratch/8793037.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:56:36] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:05:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:07:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:09:27] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:09:27] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:10:20] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:10:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:10:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:11:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:11:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:12:24] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:12:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:13:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:13:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:13:37] Searching for junctions via segment mapping
[2018-10-13 06:24:23] Retrieving sequences for splices
[2018-10-13 06:26:36] Indexing splices
[2018-10-13 06:27:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:27:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:27:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:27:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:27:54] Joining segment hits
[2018-10-13 06:30:41] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:30:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:31:12] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:31:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:31:42] Joining segment hits
[2018-10-13 06:34:41] Reporting output tracks
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[2018-10-13 07:01:45] A summary of the alignment counts can be found in /scratch/8793037.1.linga/tophat2/align_summary.txt
[2018-10-13 07:01:45] Run complete: 01:06:24 elapsed