[2018-10-13 12:58:26] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 12:58:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:58:26] Checking for Bowtie index files (genome)..
[2018-10-13 12:58:26] Checking for reference FASTA file
[2018-10-13 12:58:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:58:28] Reading known junctions from GTF file
[2018-10-13 12:58:30] Preparing reads
	 left reads: min. length=100, max. length=100, 445780 kept reads (205 discarded)
	right reads: min. length=100, max. length=100, 445471 kept reads (514 discarded)
[2018-10-13 12:58:42] Building transcriptome data files /scratch/8793248.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:58:52] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:03:41] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:04:03] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:04:26] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:04:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:04:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:04:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:04:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:04:59] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:05:03] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:05:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:05:27] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:05:33] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:05:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:05:42] Searching for junctions via segment mapping
[2018-10-13 13:07:17] Retrieving sequences for splices
[2018-10-13 13:08:24] Indexing splices
[2018-10-13 13:08:34] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:08:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:08:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:08:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:08:43] Joining segment hits
[2018-10-13 13:10:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:10:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:10:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:10:10] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:10:12] Joining segment hits
[2018-10-13 13:11:28] Reporting output tracks
-----------------------------------------------
[2018-10-13 13:13:55] A summary of the alignment counts can be found in /scratch/8793248.1.p8/tophat2/align_summary.txt
[2018-10-13 13:13:55] Run complete: 00:15:28 elapsed