[2018-10-13 08:30:11] Beginning TopHat run (v2.1.1)
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[2018-10-13 08:30:11] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:30:11] Checking for Bowtie index files (genome)..
[2018-10-13 08:30:11] Checking for reference FASTA file
[2018-10-13 08:30:11] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:30:13] Reading known junctions from GTF file
[2018-10-13 08:30:15] Preparing reads
	 left reads: min. length=100, max. length=100, 1157655 kept reads (149 discarded)
	right reads: min. length=100, max. length=100, 1157332 kept reads (472 discarded)
[2018-10-13 08:30:46] Building transcriptome data files /scratch/8793118.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:30:57] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 08:35:38] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:36:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 08:37:19] Resuming TopHat pipeline with unmapped reads
[2018-10-13 08:37:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:37:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:37:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:38:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:38:10] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:38:17] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 08:38:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 08:38:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 08:39:03] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 08:39:11] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 08:39:18] Searching for junctions via segment mapping
[2018-10-13 08:43:05] Retrieving sequences for splices
[2018-10-13 08:44:13] Indexing splices
[2018-10-13 08:44:25] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:44:29] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:44:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:44:39] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:44:43] Joining segment hits
[2018-10-13 08:46:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 08:46:05] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 08:46:10] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 08:46:15] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 08:46:20] Joining segment hits
[2018-10-13 08:47:38] Reporting output tracks
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[2018-10-13 08:58:12] A summary of the alignment counts can be found in /scratch/8793118.1.p16/tophat2/align_summary.txt
[2018-10-13 08:58:12] Run complete: 00:28:00 elapsed