[2018-10-13 01:32:41] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 01:32:41] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:32:41] Checking for Bowtie index files (genome)..
[2018-10-13 01:32:41] Checking for reference FASTA file
[2018-10-13 01:32:41] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:32:46] Reading known junctions from GTF file
[2018-10-13 01:32:51] Preparing reads
	 left reads: min. length=100, max. length=100, 254111 kept reads (158 discarded)
	right reads: min. length=100, max. length=100, 253845 kept reads (424 discarded)
[2018-10-13 01:33:03] Building transcriptome data files /scratch/8792890.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 01:33:30] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 01:45:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:45:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 01:46:08] Resuming TopHat pipeline with unmapped reads
[2018-10-13 01:46:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:46:40] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:46:51] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:47:06] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:47:16] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:47:25] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 01:48:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 01:48:12] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 01:48:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 01:48:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 01:48:50] Searching for junctions via segment mapping
[2018-10-13 01:52:42] Retrieving sequences for splices
[2018-10-13 01:56:33] Indexing splices
[2018-10-13 01:56:59] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 01:57:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 01:57:11] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 01:57:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 01:57:24] Joining segment hits
[2018-10-13 02:03:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:03:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:03:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:03:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:03:37] Joining segment hits
[2018-10-13 02:07:08] Reporting output tracks
-----------------------------------------------
[2018-10-13 02:11:05] A summary of the alignment counts can be found in /scratch/8792890.1.linga/tophat2/align_summary.txt
[2018-10-13 02:11:05] Run complete: 00:38:23 elapsed