[2018-10-13 10:27:31] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 10:27:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 10:27:31] Checking for Bowtie index files (genome)..
[2018-10-13 10:27:31] Checking for reference FASTA file
[2018-10-13 10:27:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 10:27:33] Reading known junctions from GTF file
[2018-10-13 10:27:35] Preparing reads
	 left reads: min. length=100, max. length=100, 1523185 kept reads (77 discarded)
	right reads: min. length=100, max. length=100, 1522662 kept reads (600 discarded)
[2018-10-13 10:28:16] Building transcriptome data files /scratch/8793175.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 10:28:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 10:33:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:33:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 10:34:20] Resuming TopHat pipeline with unmapped reads
[2018-10-13 10:34:20] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:34:42] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:34:47] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:34:53] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:34:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:35:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 10:35:30] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 10:35:36] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 10:35:44] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 10:35:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 10:35:57] Searching for junctions via segment mapping
[2018-10-13 10:37:55] Retrieving sequences for splices
[2018-10-13 10:39:02] Indexing splices
[2018-10-13 10:39:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:39:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:39:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:39:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:39:25] Joining segment hits
[2018-10-13 10:40:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:40:45] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:40:48] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:40:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:40:53] Joining segment hits
[2018-10-13 10:42:10] Reporting output tracks
-----------------------------------------------
[2018-10-13 10:46:49] A summary of the alignment counts can be found in /scratch/8793175.1.p8/tophat2/align_summary.txt
[2018-10-13 10:46:49] Run complete: 00:19:18 elapsed