[2018-10-13 17:49:47] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 17:49:47] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:49:47] Checking for Bowtie index files (genome)..
[2018-10-13 17:49:47] Checking for reference FASTA file
[2018-10-13 17:49:47] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:49:51] Reading known junctions from GTF file
[2018-10-13 17:49:55] Preparing reads
	 left reads: min. length=100, max. length=100, 158729 kept reads (105 discarded)
	right reads: min. length=100, max. length=100, 158594 kept reads (240 discarded)
[2018-10-13 17:50:03] Building transcriptome data files /scratch/8793412.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:50:24] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:59:02] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:59:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:59:37] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:59:37] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:59:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:00:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:00:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:00:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:00:29] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:00:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:00:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:01:06] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:01:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:01:23] Searching for junctions via segment mapping
[2018-10-13 18:03:52] Retrieving sequences for splices
[2018-10-13 18:06:07] Indexing splices
[2018-10-13 18:06:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:06:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:06:34] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:06:38] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:06:43] Joining segment hits
[2018-10-13 18:08:57] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:09:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:09:05] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:09:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:09:13] Joining segment hits
[2018-10-13 18:11:58] Reporting output tracks
-----------------------------------------------
[2018-10-13 18:14:46] A summary of the alignment counts can be found in /scratch/8793412.1.linga/tophat2/align_summary.txt
[2018-10-13 18:14:46] Run complete: 00:24:59 elapsed