[2018-10-13 18:40:57] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 18:40:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:40:57] Checking for Bowtie index files (genome)..
[2018-10-13 18:40:57] Checking for reference FASTA file
[2018-10-13 18:40:57] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:40:59] Reading known junctions from GTF file
[2018-10-13 18:41:01] Preparing reads
	 left reads: min. length=100, max. length=100, 430888 kept reads (408 discarded)
	right reads: min. length=100, max. length=100, 431006 kept reads (290 discarded)
[2018-10-13 18:41:14] Building transcriptome data files /scratch/8793450.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:41:24] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:46:07] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:46:31] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:46:56] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:46:56] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:47:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:47:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:47:29] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:47:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:47:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:48:03] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:48:07] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:48:14] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:48:19] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:48:24] Searching for junctions via segment mapping
[2018-10-13 18:49:46] Retrieving sequences for splices
[2018-10-13 18:50:52] Indexing splices
[2018-10-13 18:51:03] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:51:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:51:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:51:10] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:51:13] Joining segment hits
[2018-10-13 18:52:28] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:52:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:52:33] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:52:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:52:38] Joining segment hits
[2018-10-13 18:53:53] Reporting output tracks
-----------------------------------------------
[2018-10-13 18:55:39] A summary of the alignment counts can be found in /scratch/8793450.1.p16/tophat2/align_summary.txt
[2018-10-13 18:55:39] Run complete: 00:14:42 elapsed