[2018-10-13 11:16:06] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:16:06] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:16:07] Checking for Bowtie index files (genome)..
[2018-10-13 11:16:07] Checking for reference FASTA file
[2018-10-13 11:16:07] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:16:10] Reading known junctions from GTF file
[2018-10-13 11:16:15] Preparing reads
	 left reads: min. length=100, max. length=100, 312271 kept reads (122 discarded)
	right reads: min. length=100, max. length=100, 312029 kept reads (364 discarded)
[2018-10-13 11:16:29] Building transcriptome data files /scratch/8793198.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:16:49] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:24:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:25:08] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:25:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:25:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:25:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:26:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:26:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:26:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:26:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:26:54] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:27:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:27:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:27:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:27:30] Searching for junctions via segment mapping
[2018-10-13 11:30:24] Retrieving sequences for splices
[2018-10-13 11:32:31] Indexing splices
[2018-10-13 11:32:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:32:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:33:01] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:33:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:33:09] Joining segment hits
[2018-10-13 11:35:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:35:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:35:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:35:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:35:35] Joining segment hits
[2018-10-13 11:38:19] Reporting output tracks
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[2018-10-13 11:42:35] A summary of the alignment counts can be found in /scratch/8793198.1.linga/tophat2/align_summary.txt
[2018-10-13 11:42:35] Run complete: 00:26:28 elapsed