[2018-10-13 07:06:16] Beginning TopHat run (v2.1.1)
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[2018-10-13 07:06:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 07:06:16] Checking for Bowtie index files (genome)..
[2018-10-13 07:06:16] Checking for reference FASTA file
[2018-10-13 07:06:16] Generating SAM header for Bowtie2Index/genome
[2018-10-13 07:06:18] Reading known junctions from GTF file
[2018-10-13 07:06:20] Preparing reads
	 left reads: min. length=100, max. length=100, 757472 kept reads (180 discarded)
	right reads: min. length=100, max. length=100, 757286 kept reads (366 discarded)
[2018-10-13 07:06:40] Building transcriptome data files /scratch/8793077.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 07:06:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 07:11:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:12:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 07:13:06] Resuming TopHat pipeline with unmapped reads
[2018-10-13 07:13:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:13:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:13:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:13:34] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:13:39] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:13:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 07:14:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 07:14:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 07:14:15] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 07:14:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 07:14:27] Searching for junctions via segment mapping
[2018-10-13 07:18:14] Retrieving sequences for splices
[2018-10-13 07:19:22] Indexing splices
[2018-10-13 07:19:35] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:19:38] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:19:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:19:46] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:19:50] Joining segment hits
[2018-10-13 07:21:06] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 07:21:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 07:21:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 07:21:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 07:21:24] Joining segment hits
[2018-10-13 07:22:39] Reporting output tracks
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[2018-10-13 07:34:03] A summary of the alignment counts can be found in /scratch/8793077.1.p16/tophat2/align_summary.txt
[2018-10-13 07:34:03] Run complete: 00:27:46 elapsed