[2018-10-13 15:37:03] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 15:37:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 15:37:03] Checking for Bowtie index files (genome)..
[2018-10-13 15:37:03] Checking for reference FASTA file
[2018-10-13 15:37:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 15:37:08] Reading known junctions from GTF file
[2018-10-13 15:37:12] Preparing reads
	 left reads: min. length=100, max. length=100, 282877 kept reads (195 discarded)
	right reads: min. length=100, max. length=100, 282351 kept reads (721 discarded)
[2018-10-13 15:37:27] Building transcriptome data files /scratch/8793325.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 15:37:46] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 15:45:59] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:46:23] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 15:46:45] Resuming TopHat pipeline with unmapped reads
[2018-10-13 15:46:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:47:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:47:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:47:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:47:28] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:47:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 15:48:02] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 15:48:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 15:48:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 15:48:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 15:48:43] Searching for junctions via segment mapping
[2018-10-13 15:51:20] Retrieving sequences for splices
[2018-10-13 15:53:29] Indexing splices
[2018-10-13 15:53:56] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:54:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:54:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:54:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:54:13] Joining segment hits
[2018-10-13 15:56:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 15:56:31] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 15:56:36] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 15:56:40] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 15:56:45] Joining segment hits
[2018-10-13 15:59:14] Reporting output tracks
-----------------------------------------------
[2018-10-13 16:02:39] A summary of the alignment counts can be found in /scratch/8793325.1.linga/tophat2/align_summary.txt
[2018-10-13 16:02:39] Run complete: 00:25:35 elapsed