[2018-10-13 18:13:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:13:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:13:08] Checking for Bowtie index files (genome)..
[2018-10-13 18:13:08] Checking for reference FASTA file
[2018-10-13 18:13:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:13:13] Reading known junctions from GTF file
[2018-10-13 18:13:18] Preparing reads
	 left reads: min. length=100, max. length=100, 518865 kept reads (248 discarded)
	right reads: min. length=100, max. length=100, 518483 kept reads (630 discarded)
[2018-10-13 18:13:40] Building transcriptome data files /scratch/8793430.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:14:00] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:22:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:23:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:24:01] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:24:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:24:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:24:57] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:25:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:25:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:25:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:26:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:26:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:26:44] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:26:55] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:27:06] Searching for junctions via segment mapping
[2018-10-13 18:30:02] Retrieving sequences for splices
[2018-10-13 18:32:13] Indexing splices
[2018-10-13 18:32:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:32:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:32:41] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:32:45] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:32:50] Joining segment hits
[2018-10-13 18:35:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:35:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:35:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:35:29] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:35:34] Joining segment hits
[2018-10-13 18:37:56] Reporting output tracks
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[2018-10-13 18:41:38] A summary of the alignment counts can be found in /scratch/8793430.1.linga/tophat2/align_summary.txt
[2018-10-13 18:41:38] Run complete: 00:28:30 elapsed