[2017-06-14 21:34:35] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:35] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:35] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:35] Checking for reference FASTA file
[2017-06-14 21:34:35] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:40] Reading known junctions from GTF file
[2017-06-14 21:34:43] Preparing reads
	 left reads: min. length=101, max. length=101, 20646293 kept reads (7511 discarded)
	right reads: min. length=101, max. length=101, 20635670 kept reads (18134 discarded)
[2017-06-14 21:56:19] Building transcriptome data files /scratch/9328369.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:56:39] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:58:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:13:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:27:26] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:27:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:40:38] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:42:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:45:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:48:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:51:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 23:04:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 23:07:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 23:09:47] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 23:14:07] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:17:41] Searching for junctions via segment mapping
[2017-06-14 23:36:43] Retrieving sequences for splices
[2017-06-14 23:39:20] Indexing splices
[2017-06-14 23:40:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:41:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:43:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:44:25] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:45:36] Joining segment hits
[2017-06-14 23:49:56] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:51:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:52:32] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:53:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:55:15] Joining segment hits
[2017-06-14 23:59:08] Reporting output tracks
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[2017-06-15 00:28:12] A summary of the alignment counts can be found in /scratch/9328369.1.linga/tophat2/align_summary.txt
[2017-06-15 00:28:12] Run complete: 02:53:36 elapsed