[2018-10-13 08:52:21] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 08:52:21] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 08:52:21] Checking for Bowtie index files (genome)..
[2018-10-13 08:52:21] Checking for reference FASTA file
[2018-10-13 08:52:21] Generating SAM header for Bowtie2Index/genome
[2018-10-13 08:52:24] Reading known junctions from GTF file
[2018-10-13 08:52:29] Preparing reads
	 left reads: min. length=100, max. length=100, 1192634 kept reads (85 discarded)
	right reads: min. length=100, max. length=100, 1192340 kept reads (379 discarded)
[2018-10-13 08:53:18] Building transcriptome data files /scratch/8793128.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 08:53:37] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:01:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:02:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:03:01] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:03:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:03:43] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:03:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:04:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:04:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:04:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:05:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:05:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:05:45] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:05:58] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:06:11] Searching for junctions via segment mapping
[2018-10-13 09:11:48] Retrieving sequences for splices
[2018-10-13 09:14:04] Indexing splices
[2018-10-13 09:14:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:14:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:14:44] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:14:51] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:14:59] Joining segment hits
[2018-10-13 09:17:48] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:17:55] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:18:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:18:11] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:18:18] Joining segment hits
[2018-10-13 09:21:02] Reporting output tracks
-----------------------------------------------
[2018-10-13 09:33:11] A summary of the alignment counts can be found in /scratch/8793128.1.linga/tophat2/align_summary.txt
[2018-10-13 09:33:11] Run complete: 00:40:49 elapsed