[2018-10-13 12:35:33] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 12:35:33] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:35:33] Checking for Bowtie index files (genome)..
[2018-10-13 12:35:33] Checking for reference FASTA file
[2018-10-13 12:35:33] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:35:38] Reading known junctions from GTF file
[2018-10-13 12:35:43] Preparing reads
	 left reads: min. length=100, max. length=100, 1454540 kept reads (118 discarded)
	right reads: min. length=100, max. length=100, 1454156 kept reads (502 discarded)
[2018-10-13 12:36:51] Building transcriptome data files /scratch/8793238.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:37:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:45:39] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:47:45] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:49:48] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:49:48] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:50:38] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:50:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:51:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:51:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:51:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:52:35] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:52:49] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:53:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:53:26] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:53:43] Searching for junctions via segment mapping
[2018-10-13 13:01:00] Retrieving sequences for splices
[2018-10-13 13:03:29] Indexing splices
[2018-10-13 13:03:54] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:04:02] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:04:12] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:04:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:04:32] Joining segment hits
[2018-10-13 13:07:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:07:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:07:31] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:07:42] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:07:53] Joining segment hits
[2018-10-13 13:10:37] Reporting output tracks
-----------------------------------------------
[2018-10-13 13:31:22] A summary of the alignment counts can be found in /scratch/8793238.1.linga/tophat2/align_summary.txt
[2018-10-13 13:31:22] Run complete: 00:55:49 elapsed