[2018-10-13 10:04:16] Beginning TopHat run (v2.1.1)
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[2018-10-13 10:04:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:04:16] Checking for Bowtie index files (genome)..
[2018-10-13 10:04:16] Checking for reference FASTA file
[2018-10-13 10:04:16] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:04:18] Reading known junctions from GTF file
[2018-10-13 10:04:21] Preparing reads
	 left reads: min. length=100, max. length=100, 992964 kept reads (155 discarded)
	right reads: min. length=100, max. length=100, 992688 kept reads (431 discarded)
[2018-10-13 10:04:46] Building transcriptome data files /scratch/8793167.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:04:56] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:09:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:10:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:10:42] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:10:42] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:11:03] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:11:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:11:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:11:19] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:11:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:11:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:11:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:11:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:12:05] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:12:10] Searching for junctions via segment mapping
[2018-10-13 10:14:10] Retrieving sequences for splices
[2018-10-13 10:15:17] Indexing splices
[2018-10-13 10:15:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:15:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:15:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:15:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:15:40] Joining segment hits
[2018-10-13 10:16:56] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:16:58] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:17:01] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:17:04] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:17:07] Joining segment hits
[2018-10-13 10:18:23] Reporting output tracks
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[2018-10-13 10:23:25] A summary of the alignment counts can be found in /scratch/8793167.1.p8/tophat2/align_summary.txt
[2018-10-13 10:23:25] Run complete: 00:19:08 elapsed