[2018-10-13 14:16:55] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 14:16:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:16:55] Checking for Bowtie index files (genome)..
[2018-10-13 14:16:55] Checking for reference FASTA file
[2018-10-13 14:16:55] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:16:57] Reading known junctions from GTF file
[2018-10-13 14:16:59] Preparing reads
	 left reads: min. length=100, max. length=100, 256374 kept reads (20 discarded)
	right reads: min. length=100, max. length=100, 256288 kept reads (106 discarded)
[2018-10-13 14:17:06] Building transcriptome data files /scratch/8793286.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:17:17] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:22:51] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:23:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:23:19] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:23:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:23:30] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:23:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:23:38] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:24:01] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:24:12] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:24:26] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:24:30] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:24:35] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:24:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:24:44] Searching for junctions via segment mapping
[2018-10-13 14:26:10] Retrieving sequences for splices
[2018-10-13 14:27:22] Indexing splices
[2018-10-13 14:27:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:27:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:27:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:27:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:27:43] Joining segment hits
[2018-10-13 14:28:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:28:59] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:29:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:29:04] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:29:06] Joining segment hits
[2018-10-13 14:30:20] Reporting output tracks
-----------------------------------------------
[2018-10-13 14:32:03] A summary of the alignment counts can be found in /scratch/8793286.1.c/tophat2/align_summary.txt
[2018-10-13 14:32:03] Run complete: 00:15:08 elapsed