[2018-10-13 03:55:57] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:55:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:55:57] Checking for Bowtie index files (genome)..
[2018-10-13 03:55:57] Checking for reference FASTA file
[2018-10-13 03:55:57] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:56:01] Reading known junctions from GTF file
[2018-10-13 03:56:05] Preparing reads
	 left reads: min. length=100, max. length=100, 1033935 kept reads (85 discarded)
	right reads: min. length=100, max. length=100, 1033664 kept reads (356 discarded)
[2018-10-13 03:56:49] Building transcriptome data files /scratch/8792977.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:57:09] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:05:43] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:06:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:07:18] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:07:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:07:45] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:07:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:08:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:08:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:08:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:08:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:09:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:09:12] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:09:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:09:32] Searching for junctions via segment mapping
[2018-10-13 04:13:18] Retrieving sequences for splices
[2018-10-13 04:15:37] Indexing splices
[2018-10-13 04:15:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:16:03] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:16:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:16:14] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:16:19] Joining segment hits
[2018-10-13 04:18:54] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:18:59] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:19:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:19:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:19:16] Joining segment hits
[2018-10-13 04:21:57] Reporting output tracks
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[2018-10-13 04:30:49] A summary of the alignment counts can be found in /scratch/8792977.1.linga/tophat2/align_summary.txt
[2018-10-13 04:30:49] Run complete: 00:34:52 elapsed