[2018-10-12 23:31:57] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:31:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:31:57] Checking for Bowtie index files (genome)..
[2018-10-12 23:31:57] Checking for reference FASTA file
[2018-10-12 23:31:57] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:32:02] Reading known junctions from GTF file
[2018-10-12 23:32:06] Preparing reads
	 left reads: min. length=100, max. length=100, 180654 kept reads (74 discarded)
	right reads: min. length=100, max. length=100, 180453 kept reads (275 discarded)
[2018-10-12 23:32:14] Building transcriptome data files /scratch/8792837.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:32:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:40:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:40:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:41:23] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:41:25] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:41:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:42:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:42:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:42:28] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:42:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:43:10] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:43:19] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:43:31] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:43:41] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:43:50] Searching for junctions via segment mapping
[2018-10-12 23:46:16] Retrieving sequences for splices
[2018-10-12 23:48:53] Indexing splices
[2018-10-12 23:49:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:49:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:49:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:49:27] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:49:31] Joining segment hits
[2018-10-12 23:51:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:51:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:51:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:51:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:52:02] Joining segment hits
[2018-10-12 23:54:24] Reporting output tracks
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[2018-10-12 23:57:10] A summary of the alignment counts can be found in /scratch/8792837.1.linga/tophat2/align_summary.txt
[2018-10-12 23:57:10] Run complete: 00:25:13 elapsed