[2017-06-14 21:34:42] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:42] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:43] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:43] Checking for reference FASTA file
[2017-06-14 21:34:43] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:47] Reading known junctions from GTF file
[2017-06-14 21:34:50] Preparing reads
	 left reads: min. length=101, max. length=101, 18974336 kept reads (68 discarded)
	right reads: min. length=101, max. length=101, 18925366 kept reads (49038 discarded)
[2017-06-14 21:54:50] Building transcriptome data files /scratch/9328374.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:55:06] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:56:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:10:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:23:12] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:23:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:35:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:37:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:39:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:41:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:44:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:58:12] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 23:01:13] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 23:04:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 23:08:14] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:12:23] Searching for junctions via segment mapping
[2017-06-14 23:29:25] Retrieving sequences for splices
[2017-06-14 23:31:46] Indexing splices
[2017-06-14 23:32:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:33:27] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:34:33] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:35:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:36:42] Joining segment hits
[2017-06-14 23:40:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:41:37] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:43:01] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:44:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:45:54] Joining segment hits
[2017-06-14 23:50:02] Reporting output tracks
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[2017-06-15 00:16:12] A summary of the alignment counts can be found in /scratch/9328374.1.linga/tophat2/align_summary.txt
[2017-06-15 00:16:12] Run complete: 02:41:29 elapsed