[2018-10-13 11:39:05] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 11:39:05] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:39:05] Checking for Bowtie index files (genome)..
[2018-10-13 11:39:05] Checking for reference FASTA file
[2018-10-13 11:39:05] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:39:09] Reading known junctions from GTF file
[2018-10-13 11:39:13] Preparing reads
	 left reads: min. length=100, max. length=100, 1734287 kept reads (86 discarded)
	right reads: min. length=100, max. length=100, 1733901 kept reads (472 discarded)
[2018-10-13 11:40:24] Building transcriptome data files /scratch/8793208.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:40:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:48:36] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:49:57] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:51:21] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:51:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:52:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:52:09] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:52:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:52:34] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:52:46] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:53:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:53:41] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:53:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:54:09] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:54:22] Searching for junctions via segment mapping
[2018-10-13 11:59:10] Retrieving sequences for splices
[2018-10-13 12:01:35] Indexing splices
[2018-10-13 12:02:01] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:02:08] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:02:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:02:23] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:02:31] Joining segment hits
[2018-10-13 12:05:12] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:05:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:05:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:05:36] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:05:44] Joining segment hits
[2018-10-13 12:08:50] Reporting output tracks
-----------------------------------------------
[2018-10-13 12:24:57] A summary of the alignment counts can be found in /scratch/8793208.1.linga/tophat2/align_summary.txt
[2018-10-13 12:24:57] Run complete: 00:45:52 elapsed