[2018-10-13 13:34:41] Beginning TopHat run (v2.1.1)
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[2018-10-13 13:34:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:34:41] Checking for Bowtie index files (genome)..
[2018-10-13 13:34:41] Checking for reference FASTA file
[2018-10-13 13:34:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:34:45] Reading known junctions from GTF file
[2018-10-13 13:34:49] Preparing reads
	 left reads: min. length=100, max. length=100, 918158 kept reads (290 discarded)
	right reads: min. length=100, max. length=100, 918024 kept reads (424 discarded)
[2018-10-13 13:35:28] Building transcriptome data files /scratch/8793264.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:35:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:43:15] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:44:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:45:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:45:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:46:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:46:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:47:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:47:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:47:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:48:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:48:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:49:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:49:28] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:49:43] Searching for junctions via segment mapping
[2018-10-13 13:59:30] Retrieving sequences for splices
[2018-10-13 14:01:45] Indexing splices
[2018-10-13 14:02:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:02:20] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:02:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:02:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:02:57] Joining segment hits
[2018-10-13 14:05:23] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:05:33] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:05:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:06:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:06:11] Joining segment hits
[2018-10-13 14:08:40] Reporting output tracks
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[2018-10-13 14:26:23] A summary of the alignment counts can be found in /scratch/8793264.1.linga/tophat2/align_summary.txt
[2018-10-13 14:26:23] Run complete: 00:51:42 elapsed