[2018-10-13 03:13:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:13:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:13:10] Checking for Bowtie index files (genome)..
[2018-10-13 03:13:10] Checking for reference FASTA file
[2018-10-13 03:13:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:13:14] Reading known junctions from GTF file
[2018-10-13 03:13:19] Preparing reads
	 left reads: min. length=100, max. length=100, 286777 kept reads (196 discarded)
	right reads: min. length=100, max. length=100, 286631 kept reads (342 discarded)
[2018-10-13 03:13:34] Building transcriptome data files /scratch/8792947.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:13:53] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:22:24] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:22:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:23:24] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:23:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:23:57] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:24:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:24:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:24:29] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:24:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:25:13] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:25:23] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:25:35] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:25:45] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:25:55] Searching for junctions via segment mapping
[2018-10-13 03:28:23] Retrieving sequences for splices
[2018-10-13 03:30:24] Indexing splices
[2018-10-13 03:30:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:30:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:30:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:30:56] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:31:00] Joining segment hits
[2018-10-13 03:33:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:33:11] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:33:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:33:20] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:33:24] Joining segment hits
[2018-10-13 03:35:33] Reporting output tracks
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[2018-10-13 03:38:38] A summary of the alignment counts can be found in /scratch/8792947.1.linga/tophat2/align_summary.txt
[2018-10-13 03:38:38] Run complete: 00:25:28 elapsed