[2017-06-14 21:34:25] Beginning TopHat run (v2.1.1)
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[2017-06-14 21:34:25] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-14 21:34:25] Checking for Bowtie index files (genome)..
[2017-06-14 21:34:25] Checking for reference FASTA file
[2017-06-14 21:34:25] Generating SAM header for Bowtie2Index/genome
[2017-06-14 21:34:29] Reading known junctions from GTF file
[2017-06-14 21:34:32] Preparing reads
	 left reads: min. length=101, max. length=101, 46023193 kept reads (241294 discarded)
	right reads: min. length=101, max. length=101, 46237018 kept reads (27469 discarded)
[2017-06-14 22:28:21] Building transcriptome data files /scratch/9328372.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-14 22:28:42] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-14 22:30:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 23:03:33] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-14 23:36:55] Resuming TopHat pipeline with unmapped reads
[2017-06-14 23:36:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-15 00:02:09] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-15 00:06:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-15 00:11:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-15 00:15:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-15 00:21:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-15 00:46:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-15 00:52:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-15 00:58:04] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-15 01:04:18] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-15 01:11:25] Searching for junctions via segment mapping
[2017-06-15 02:01:20] Retrieving sequences for splices
[2017-06-15 02:03:41] Indexing splices
[2017-06-15 02:04:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-15 02:08:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-15 02:12:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-15 02:15:35] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-15 02:19:25] Joining segment hits
[2017-06-15 02:24:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-15 02:27:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-15 02:32:00] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-15 02:36:02] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-15 02:40:05] Joining segment hits
[2017-06-15 02:45:14] Reporting output tracks
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[2017-06-15 03:42:17] A summary of the alignment counts can be found in /scratch/9328372.1.linga/tophat2/align_summary.txt
[2017-06-15 03:42:17] Run complete: 06:07:51 elapsed