[2018-10-13 11:11:41] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:11:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:11:41] Checking for Bowtie index files (genome)..
[2018-10-13 11:11:41] Checking for reference FASTA file
[2018-10-13 11:11:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:11:43] Reading known junctions from GTF file
[2018-10-13 11:11:46] Preparing reads
	 left reads: min. length=100, max. length=100, 913845 kept reads (271 discarded)
	right reads: min. length=100, max. length=100, 913531 kept reads (585 discarded)
[2018-10-13 11:12:12] Building transcriptome data files /scratch/8793197.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:12:22] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:17:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:17:51] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:18:37] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:18:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:19:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:19:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:19:17] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:19:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:19:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:19:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:20:05] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:20:15] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:20:23] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:20:31] Searching for junctions via segment mapping
[2018-10-13 11:25:06] Retrieving sequences for splices
[2018-10-13 11:26:13] Indexing splices
[2018-10-13 11:26:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:26:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:26:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:26:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:26:46] Joining segment hits
[2018-10-13 11:28:03] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:28:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:28:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:28:19] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:28:23] Joining segment hits
[2018-10-13 11:29:41] Reporting output tracks
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[2018-10-13 11:39:29] A summary of the alignment counts can be found in /scratch/8793197.1.p16/tophat2/align_summary.txt
[2018-10-13 11:39:29] Run complete: 00:27:48 elapsed