[2017-06-16 10:20:08] Beginning TopHat run (v2.1.1)
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[2017-06-16 10:20:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:20:08] Checking for Bowtie index files (genome)..
[2017-06-16 10:20:08] Checking for reference FASTA file
[2017-06-16 10:20:08] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:20:13] Reading known junctions from GTF file
[2017-06-16 10:20:16] Preparing reads
	 left reads: min. length=101, max. length=101, 21452635 kept reads (3383 discarded)
	right reads: min. length=101, max. length=101, 21441574 kept reads (14444 discarded)
[2017-06-16 10:42:51] Building transcriptome data files /scratch/9351460.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 10:43:10] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 10:45:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 10:59:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 11:14:07] Resuming TopHat pipeline with unmapped reads
[2017-06-16 11:14:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:27:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:29:28] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:31:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:34:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:37:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:49:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:51:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:54:18] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:57:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 12:01:12] Searching for junctions via segment mapping
[2017-06-16 12:35:56] Retrieving sequences for splices
[2017-06-16 12:38:24] Indexing splices
[2017-06-16 12:39:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:41:22] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:43:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:45:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:47:18] Joining segment hits
[2017-06-16 12:51:40] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:53:47] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:55:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:57:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:59:58] Joining segment hits
[2017-06-16 13:04:07] Reporting output tracks
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[2017-06-16 13:33:00] A summary of the alignment counts can be found in /scratch/9351460.1.linga/tophat2/align_summary.txt
[2017-06-16 13:33:00] Run complete: 03:12:51 elapsed