[2018-10-13 02:12:00] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:12:00] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:12:00] Checking for Bowtie index files (genome)..
[2018-10-13 02:12:00] Checking for reference FASTA file
[2018-10-13 02:12:00] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:12:05] Reading known junctions from GTF file
[2018-10-13 02:12:09] Preparing reads
	 left reads: min. length=100, max. length=100, 115861 kept reads (160 discarded)
	right reads: min. length=100, max. length=100, 115770 kept reads (251 discarded)
[2018-10-13 02:12:14] Building transcriptome data files /scratch/8792908.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:12:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:20:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:20:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:21:16] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:21:17] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:21:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:21:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:21:57] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:22:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:22:14] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:22:37] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:22:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:22:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:23:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:23:14] Searching for junctions via segment mapping
[2018-10-13 02:25:28] Retrieving sequences for splices
[2018-10-13 02:27:33] Indexing splices
[2018-10-13 02:27:56] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:28:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:28:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:28:08] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:28:12] Joining segment hits
[2018-10-13 02:30:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:30:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:30:30] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:30:34] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:30:38] Joining segment hits
[2018-10-13 02:33:07] Reporting output tracks
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[2018-10-13 02:35:47] A summary of the alignment counts can be found in /scratch/8792908.1.linga/tophat2/align_summary.txt
[2018-10-13 02:35:47] Run complete: 00:23:47 elapsed