[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, 18294739 kept reads (5704 discarded)
	right reads: min. length=101, max. length=101, 18281347 kept reads (19096 discarded)
[2017-06-14 21:53:56] Building transcriptome data files /scratch/9328370.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:54:11] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:55:56] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:08:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:21:14] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:21:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:32:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:35:03] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:37:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:39:15] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:41:59] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:54:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:56:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:59:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 23:02:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:05:52] Searching for junctions via segment mapping
[2017-06-14 23:43:11] Retrieving sequences for splices
[2017-06-14 23:45:44] Indexing splices
[2017-06-14 23:46:32] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-14 23:48:28] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-14 23:50:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-14 23:52:12] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-14 23:54:08] Joining segment hits
[2017-06-14 23:58:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-15 00:00:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-15 00:02:01] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-15 00:04:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-15 00:06:09] Joining segment hits
[2017-06-15 00:10:17] Reporting output tracks
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[2017-06-15 00:36:22] A summary of the alignment counts can be found in /scratch/9328370.1.linga/tophat2/align_summary.txt
[2017-06-15 00:36:22] Run complete: 03:01:47 elapsed