[2018-10-12 23:29:17] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:29:17] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:29:17] Checking for Bowtie index files (genome)..
[2018-10-12 23:29:17] Checking for reference FASTA file
[2018-10-12 23:29:17] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:29:22] Reading known junctions from GTF file
[2018-10-12 23:29:26] Preparing reads
	 left reads: min. length=100, max. length=100, 301709 kept reads (230 discarded)
	right reads: min. length=100, max. length=100, 301464 kept reads (475 discarded)
[2018-10-12 23:29:39] Building transcriptome data files /scratch/8792836.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:29:59] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:37:53] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:38:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:38:56] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:38:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:39:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:39:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:39:53] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:40:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:40:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:40:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:40:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:41:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:42:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:44:16] Searching for junctions via segment mapping
[2018-10-12 23:47:06] Retrieving sequences for splices
[2018-10-12 23:49:17] Indexing splices
[2018-10-12 23:49:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:49:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:49:44] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:49:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:49:52] Joining segment hits
[2018-10-12 23:52:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:52:15] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:52:19] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:52:23] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:52:27] Joining segment hits
[2018-10-12 23:54:37] Reporting output tracks
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[2018-10-12 23:58:02] A summary of the alignment counts can be found in /scratch/8792836.1.linga/tophat2/align_summary.txt
[2018-10-12 23:58:02] Run complete: 00:28:45 elapsed