[2018-10-12 23:00:57] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:00:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:00:57] Checking for Bowtie index files (genome)..
[2018-10-12 23:00:57] Checking for reference FASTA file
[2018-10-12 23:00:57] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:01:02] Reading known junctions from GTF file
[2018-10-12 23:01:06] Preparing reads
	 left reads: min. length=100, max. length=100, 279754 kept reads (148 discarded)
	right reads: min. length=100, max. length=100, 279433 kept reads (469 discarded)
[2018-10-12 23:01:20] Building transcriptome data files /scratch/8792815.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:01:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:10:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:11:20] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:11:51] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:11:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:12:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:12:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:12:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:12:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:13:04] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:13:38] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:13:48] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:13:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:14:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:14:19] Searching for junctions via segment mapping
[2018-10-12 23:17:01] Retrieving sequences for splices
[2018-10-12 23:19:16] Indexing splices
[2018-10-12 23:19:38] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:19:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:19:46] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:19:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:19:55] Joining segment hits
[2018-10-12 23:22:15] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:22:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:22:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:22:27] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:22:31] Joining segment hits
[2018-10-12 23:24:53] Reporting output tracks
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[2018-10-12 23:28:30] A summary of the alignment counts can be found in /scratch/8792815.1.linga/tophat2/align_summary.txt
[2018-10-12 23:28:30] Run complete: 00:27:32 elapsed