[2018-10-13 17:32:28] Beginning TopHat run (v2.1.1)
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[2018-10-13 17:32:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:32:28] Checking for Bowtie index files (genome)..
[2018-10-13 17:32:28] Checking for reference FASTA file
[2018-10-13 17:32:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:32:32] Reading known junctions from GTF file
[2018-10-13 17:32:37] Preparing reads
	 left reads: min. length=100, max. length=100, 255923 kept reads (377 discarded)
	right reads: min. length=100, max. length=100, 255711 kept reads (589 discarded)
[2018-10-13 17:32:48] Building transcriptome data files /scratch/8793402.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:33:07] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:41:34] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:42:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:42:41] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:42:41] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:43:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:43:19] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:43:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:43:41] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:43:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:44:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:44:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:44:39] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:44:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:44:59] Searching for junctions via segment mapping
[2018-10-13 17:47:43] Retrieving sequences for splices
[2018-10-13 17:49:54] Indexing splices
[2018-10-13 17:50:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:50:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:50:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:50:26] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:50:30] Joining segment hits
[2018-10-13 17:53:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:53:13] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:53:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:53:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:53:26] Joining segment hits
[2018-10-13 17:55:43] Reporting output tracks
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[2018-10-13 17:58:38] A summary of the alignment counts can be found in /scratch/8793402.1.linga/tophat2/align_summary.txt
[2018-10-13 17:58:38] Run complete: 00:26:09 elapsed