[2017-06-14 21:34:31] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:32] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:32] Checking for reference FASTA file
[2017-06-14 21:34:32] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:36] Reading known junctions from GTF file
[2017-06-14 21:34:38] Preparing reads
	 left reads: min. length=101, max. length=101, 19617219 kept reads (4830 discarded)
	right reads: min. length=101, max. length=101, 19610609 kept reads (11440 discarded)
[2017-06-14 21:55:16] Building transcriptome data files /scratch/9328373.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 21:55:31] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 21:57:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:09:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 22:21:45] Resuming TopHat pipeline with unmapped reads
[2017-06-14 22:21:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 22:36:26] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 22:39:39] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 22:43:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 22:46:19] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 22:50:08] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-14 23:02:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-14 23:05:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-14 23:08:49] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-14 23:12:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-14 23:16:09] Searching for junctions via segment mapping
[2017-06-15 00:40:02] Retrieving sequences for splices
[2017-06-15 00:42:20] Indexing splices
[2017-06-15 00:43:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-15 00:47:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-15 00:51:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-15 00:55:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-15 00:59:00] Joining segment hits
[2017-06-15 01:04:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-15 01:08:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-15 01:12:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-15 01:16:08] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-15 01:20:40] Joining segment hits
[2017-06-15 01:25:57] Reporting output tracks
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[2017-06-15 01:52:52] A summary of the alignment counts can be found in /scratch/9328373.1.linga/tophat2/align_summary.txt
[2017-06-15 01:52:52] Run complete: 04:18:20 elapsed