[2018-10-13 06:39:34] Beginning TopHat run (v2.1.1)
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[2018-10-13 06:39:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:39:34] Checking for Bowtie index files (genome)..
[2018-10-13 06:39:34] Checking for reference FASTA file
[2018-10-13 06:39:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:39:39] Reading known junctions from GTF file
[2018-10-13 06:39:43] Preparing reads
	 left reads: min. length=100, max. length=100, 1408141 kept reads (82 discarded)
	right reads: min. length=100, max. length=100, 1407606 kept reads (617 discarded)
[2018-10-13 06:40:43] Building transcriptome data files /scratch/8793062.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:41:03] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:49:46] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:50:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:52:04] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:52:04] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:52:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:52:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:53:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:53:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:53:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:54:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:54:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:54:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:54:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:54:57] Searching for junctions via segment mapping
[2018-10-13 06:59:04] Retrieving sequences for splices
[2018-10-13 07:01:13] Indexing splices
[2018-10-13 07:01:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:01:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:01:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:01:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:02:05] Joining segment hits
[2018-10-13 07:04:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:04:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:04:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:04:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:05:02] Joining segment hits
[2018-10-13 07:07:35] Reporting output tracks
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[2018-10-13 07:22:10] A summary of the alignment counts can be found in /scratch/8793062.1.linga/tophat2/align_summary.txt
[2018-10-13 07:22:10] Run complete: 00:42:35 elapsed