[2018-10-13 00:16:26] Beginning TopHat run (v2.1.1)
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[2018-10-13 00:16:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 00:16:26] Checking for Bowtie index files (genome)..
[2018-10-13 00:16:26] Checking for reference FASTA file
[2018-10-13 00:16:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 00:16:31] Reading known junctions from GTF file
[2018-10-13 00:16:36] Preparing reads
	 left reads: min. length=100, max. length=100, 435568 kept reads (247 discarded)
	right reads: min. length=100, max. length=100, 435014 kept reads (801 discarded)
[2018-10-13 00:16:57] Building transcriptome data files /scratch/8792861.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 00:17:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 00:26:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:27:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 00:27:57] Resuming TopHat pipeline with unmapped reads
[2018-10-13 00:27:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:28:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:29:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:29:20] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:29:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:29:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 00:30:42] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 00:30:53] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 00:31:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 00:31:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 00:31:33] Searching for junctions via segment mapping
[2018-10-13 00:34:42] Retrieving sequences for splices
[2018-10-13 00:37:11] Indexing splices
[2018-10-13 00:37:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:37:41] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:37:49] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:37:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:37:59] Joining segment hits
[2018-10-13 00:40:31] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 00:40:36] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 00:40:41] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 00:40:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 00:40:51] Joining segment hits
[2018-10-13 00:43:31] Reporting output tracks
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[2018-10-13 00:47:50] A summary of the alignment counts can be found in /scratch/8792861.1.linga/tophat2/align_summary.txt
[2018-10-13 00:47:50] Run complete: 00:31:23 elapsed