[2018-10-12 21:56:11] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-12 21:56:11] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 21:56:11] Checking for Bowtie index files (genome)..
[2018-10-12 21:56:11] Checking for reference FASTA file
[2018-10-12 21:56:11] Generating SAM header for Bowtie2Index/genome
[2018-10-12 21:56:13] Reading known junctions from GTF file
[2018-10-12 21:56:15] Preparing reads
	 left reads: min. length=100, max. length=100, 321638 kept reads (221 discarded)
	right reads: min. length=100, max. length=100, 321341 kept reads (518 discarded)
[2018-10-12 21:56:25] Building transcriptome data files /scratch/8792773.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 21:56:35] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:01:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:01:37] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:01:57] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:01:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:02:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:02:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:02:28] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:02:32] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:02:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:02:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:03:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:03:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:03:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:03:18] Searching for junctions via segment mapping
[2018-10-12 22:04:37] Retrieving sequences for splices
[2018-10-12 22:05:44] Indexing splices
[2018-10-12 22:05:55] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:05:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:05:59] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:06:02] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:06:04] Joining segment hits
[2018-10-12 22:07:20] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:07:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:07:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:07:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:07:28] Joining segment hits
[2018-10-12 22:08:44] Reporting output tracks
-----------------------------------------------
[2018-10-12 22:10:22] A summary of the alignment counts can be found in /scratch/8792773.1.p16/tophat2/align_summary.txt
[2018-10-12 22:10:22] Run complete: 00:14:11 elapsed