[2018-10-13 15:46:53] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 15:46:53] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:46:53] Checking for Bowtie index files (genome)..
[2018-10-13 15:46:53] Checking for reference FASTA file
[2018-10-13 15:46:53] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:46:58] Reading known junctions from GTF file
[2018-10-13 15:47:02] Preparing reads
	 left reads: min. length=100, max. length=100, 121159 kept reads (171 discarded)
	right reads: min. length=100, max. length=100, 121005 kept reads (325 discarded)
[2018-10-13 15:47:07] Building transcriptome data files /scratch/8793329.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:47:27] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:54:58] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:55:15] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:55:34] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:55:34] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:55:53] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:56:01] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:56:11] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:56:20] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:56:28] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:56:48] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:56:55] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:57:04] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:57:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:57:21] Searching for junctions via segment mapping
[2018-10-13 15:59:45] Retrieving sequences for splices
[2018-10-13 16:01:54] Indexing splices
[2018-10-13 16:02:15] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:02:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:02:23] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:02:28] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:02:32] Joining segment hits
[2018-10-13 16:04:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:04:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:04:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:04:59] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:05:03] Joining segment hits
[2018-10-13 16:07:14] Reporting output tracks
-----------------------------------------------
[2018-10-13 16:09:45] A summary of the alignment counts can be found in /scratch/8793329.1.linga/tophat2/align_summary.txt
[2018-10-13 16:09:45] Run complete: 00:22:52 elapsed