[2017-06-14 21:34:18] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:18] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:18] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:18] Checking for reference FASTA file
[2017-06-14 21:34:18] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:24] Reading known junctions from GTF file
[2017-06-14 21:34:26] Preparing reads
	 left reads: min. length=101, max. length=101, 15732036 kept reads (32 discarded)
	right reads: min. length=101, max. length=101, 15689825 kept reads (42243 discarded)
[2017-06-14 21:50:06] Building transcriptome data files /scratch/9328377.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:50:22] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:52:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:02:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:13:00] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:13:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:23:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:25:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:27:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:29:19] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:31:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:45:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:48:06] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:50:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:56:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:00:28] Searching for junctions via segment mapping
[2017-06-14 23:10:55] Retrieving sequences for splices
[2017-06-14 23:13:14] Indexing splices
[2017-06-14 23:14:04] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:14:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:15:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:16:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:17:07] Joining segment hits
[2017-06-14 23:20:50] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:21:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:22:36] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:23:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:24:34] Joining segment hits
[2017-06-14 23:28:33] Reporting output tracks
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[2017-06-14 23:50:26] A summary of the alignment counts can be found in /scratch/9328377.1.linga/tophat2/align_summary.txt
[2017-06-14 23:50:26] Run complete: 02:16:08 elapsed