[2018-10-13 17:40:28] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 17:40:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 17:40:29] Checking for Bowtie index files (genome)..
[2018-10-13 17:40:29] Checking for reference FASTA file
[2018-10-13 17:40:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 17:40:34] Reading known junctions from GTF file
[2018-10-13 17:40:38] Preparing reads
	 left reads: min. length=100, max. length=100, 578782 kept reads (394 discarded)
	right reads: min. length=100, max. length=100, 578389 kept reads (787 discarded)
[2018-10-13 17:41:03] Building transcriptome data files /scratch/8793407.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 17:41:23] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 17:49:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:50:18] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 17:51:02] Resuming TopHat pipeline with unmapped reads
[2018-10-13 17:51:02] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:51:36] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:51:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:52:01] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:52:12] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:52:22] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 17:52:59] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 17:53:10] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 17:53:25] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 17:53:37] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 17:53:49] Searching for junctions via segment mapping
[2018-10-13 17:56:58] Retrieving sequences for splices
[2018-10-13 17:59:08] Indexing splices
[2018-10-13 17:59:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 17:59:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 17:59:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 17:59:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 17:59:47] Joining segment hits
[2018-10-13 18:02:13] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:02:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:02:23] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:02:28] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:02:32] Joining segment hits
[2018-10-13 18:05:39] Reporting output tracks
-----------------------------------------------
[2018-10-13 18:09:48] A summary of the alignment counts can be found in /scratch/8793407.1.linga/tophat2/align_summary.txt
[2018-10-13 18:09:48] Run complete: 00:29:19 elapsed