[2018-10-13 01:05:25] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 01:05:25] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:05:25] Checking for Bowtie index files (genome)..
[2018-10-13 01:05:25] Checking for reference FASTA file
[2018-10-13 01:05:25] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:05:27] Reading known junctions from GTF file
[2018-10-13 01:05:29] Preparing reads
	 left reads: min. length=100, max. length=100, 438553 kept reads (266 discarded)
	right reads: min. length=100, max. length=100, 438061 kept reads (758 discarded)
[2018-10-13 01:05:42] Building transcriptome data files /scratch/8792877.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:05:53] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:10:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:11:06] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:11:33] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:11:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:12:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:12:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:12:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:12:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:12:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:12:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:12:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:13:01] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:13:06] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:13:12] Searching for junctions via segment mapping
[2018-10-13 01:14:34] Retrieving sequences for splices
[2018-10-13 01:15:41] Indexing splices
[2018-10-13 01:15:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:15:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:15:57] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:15:59] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:16:01] Joining segment hits
[2018-10-13 01:17:16] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:17:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:17:21] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:17:24] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:17:26] Joining segment hits
[2018-10-13 01:18:41] Reporting output tracks
-----------------------------------------------
[2018-10-13 01:20:31] A summary of the alignment counts can be found in /scratch/8792877.1.p8/tophat2/align_summary.txt
[2018-10-13 01:20:31] Run complete: 00:15:06 elapsed