[2018-10-12 21:01:55] Beginning TopHat run (v2.1.1)
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[2018-10-12 21:01:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:01:55] Checking for Bowtie index files (genome)..
[2018-10-12 21:01:55] Checking for reference FASTA file
[2018-10-12 21:01:55] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:01:59] Reading known junctions from GTF file
[2018-10-12 21:02:04] Preparing reads
	 left reads: min. length=100, max. length=100, 297131 kept reads (200 discarded)
	right reads: min. length=100, max. length=100, 296925 kept reads (406 discarded)
[2018-10-12 21:02:19] Building transcriptome data files /scratch/8792741.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:02:39] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 21:11:12] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:11:42] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 21:12:14] Resuming TopHat pipeline with unmapped reads
[2018-10-12 21:12:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:12:46] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:12:55] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:13:08] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:13:17] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:13:27] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 21:14:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 21:14:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 21:14:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 21:14:32] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 21:14:41] Searching for junctions via segment mapping
[2018-10-12 21:17:32] Retrieving sequences for splices
[2018-10-12 21:19:47] Indexing splices
[2018-10-12 21:20:09] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:20:14] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:20:19] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:20:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:20:28] Joining segment hits
[2018-10-12 21:23:04] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 21:23:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 21:23:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 21:23:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 21:23:23] Joining segment hits
[2018-10-12 21:25:53] Reporting output tracks
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[2018-10-12 21:29:12] A summary of the alignment counts can be found in /scratch/8792741.1.linga/tophat2/align_summary.txt
[2018-10-12 21:29:12] Run complete: 00:27:17 elapsed