[2017-06-16 10:19:49] Beginning TopHat run (v2.1.1)
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[2017-06-16 10:19:49] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2017-06-16 10:19:49] Checking for Bowtie index files (genome)..
[2017-06-16 10:19:49] Checking for reference FASTA file
[2017-06-16 10:19:49] Generating SAM header for Bowtie2Index/genome
[2017-06-16 10:19:53] Reading known junctions from GTF file
[2017-06-16 10:19:56] Preparing reads
	 left reads: min. length=101, max. length=101, 23002382 kept reads (5688 discarded)
	right reads: min. length=101, max. length=101, 22994532 kept reads (13538 discarded)
[2017-06-16 10:43:01] Building transcriptome data files /scratch/9351456.1.linga/tophat2/tmp/RefSeq_GeneBody
[2017-06-16 10:43:22] Building Bowtie index from RefSeq_GeneBody.fa
[2017-06-16 10:45:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 11:01:02] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2017-06-16 11:16:30] Resuming TopHat pipeline with unmapped reads
[2017-06-16 11:16:30] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:30:12] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:32:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 11:35:48] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 11:38:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 11:42:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2017-06-16 11:55:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2017-06-16 11:58:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2017-06-16 12:01:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2017-06-16 12:04:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2017-06-16 12:08:05] Searching for junctions via segment mapping
[2017-06-16 12:36:39] Retrieving sequences for splices
[2017-06-16 12:39:02] Indexing splices
[2017-06-16 12:39:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:41:39] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:43:29] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:45:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:47:06] Joining segment hits
[2017-06-16 12:51:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2017-06-16 12:52:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2017-06-16 12:54:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2017-06-16 12:55:56] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2017-06-16 12:57:37] Joining segment hits
[2017-06-16 13:01:20] Reporting output tracks
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[2017-06-16 13:28:55] A summary of the alignment counts can be found in /scratch/9351456.1.linga/tophat2/align_summary.txt
[2017-06-16 13:28:55] Run complete: 03:09:06 elapsed