[2018-10-13 18:32:23] Beginning TopHat run (v2.1.1)
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[2018-10-13 18:32:23] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:32:23] Checking for Bowtie index files (genome)..
[2018-10-13 18:32:23] Checking for reference FASTA file
[2018-10-13 18:32:23] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:32:28] Reading known junctions from GTF file
[2018-10-13 18:32:32] Preparing reads
	 left reads: min. length=100, max. length=100, 533633 kept reads (200 discarded)
	right reads: min. length=100, max. length=100, 533343 kept reads (490 discarded)
[2018-10-13 18:32:55] Building transcriptome data files /scratch/8793441.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:33:14] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:42:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:43:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:43:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:43:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:44:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:44:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:45:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:45:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:45:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:46:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:46:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:46:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:46:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:46:56] Searching for junctions via segment mapping
[2018-10-13 18:49:57] Retrieving sequences for splices
[2018-10-13 18:52:10] Indexing splices
[2018-10-13 18:52:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:52:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:52:45] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:52:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:52:54] Joining segment hits
[2018-10-13 18:55:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:55:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:55:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:55:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:55:37] Joining segment hits
[2018-10-13 18:58:13] Reporting output tracks
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[2018-10-13 19:01:59] A summary of the alignment counts can be found in /scratch/8793441.1.linga/tophat2/align_summary.txt
[2018-10-13 19:01:59] Run complete: 00:29:35 elapsed