[2018-10-13 14:36:53] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:36:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:36:53] Checking for Bowtie index files (genome)..
[2018-10-13 14:36:53] Checking for reference FASTA file
[2018-10-13 14:36:53] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:36:58] Reading known junctions from GTF file
[2018-10-13 14:37:03] Preparing reads
	 left reads: min. length=100, max. length=100, 461730 kept reads (259 discarded)
	right reads: min. length=100, max. length=100, 461624 kept reads (365 discarded)
[2018-10-13 14:37:21] Building transcriptome data files /scratch/8793298.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:37:43] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:45:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:47:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:48:12] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:48:12] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:48:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:48:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:48:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:49:09] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:49:20] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:49:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:49:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:50:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:50:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:50:31] Searching for junctions via segment mapping
[2018-10-13 14:56:22] Retrieving sequences for splices
[2018-10-13 14:58:23] Indexing splices
[2018-10-13 14:58:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:58:53] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:59:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:59:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:59:18] Joining segment hits
[2018-10-13 15:01:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:01:43] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:01:52] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:02:00] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:02:10] Joining segment hits
[2018-10-13 15:04:35] Reporting output tracks
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[2018-10-13 15:20:12] A summary of the alignment counts can be found in /scratch/8793298.1.linga/tophat2/align_summary.txt
[2018-10-13 15:20:12] Run complete: 00:43:18 elapsed