[2018-10-13 18:24:19] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 18:24:19] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 18:24:19] Checking for Bowtie index files (genome)..
[2018-10-13 18:24:19] Checking for reference FASTA file
[2018-10-13 18:24:19] Generating SAM header for Bowtie2Index/genome
[2018-10-13 18:24:24] Reading known junctions from GTF file
[2018-10-13 18:24:28] Preparing reads
	 left reads: min. length=100, max. length=100, 526060 kept reads (294 discarded)
	right reads: min. length=100, max. length=100, 525610 kept reads (744 discarded)
[2018-10-13 18:24:52] Building transcriptome data files /scratch/8793436.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 18:25:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 18:33:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:34:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 18:35:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 18:35:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:35:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:36:00] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:36:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:36:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:36:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 18:37:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 18:37:24] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 18:37:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 18:37:49] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 18:38:00] Searching for junctions via segment mapping
[2018-10-13 18:40:52] Retrieving sequences for splices
[2018-10-13 18:42:55] Indexing splices
[2018-10-13 18:43:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:43:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:43:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:43:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:43:33] Joining segment hits
[2018-10-13 18:45:53] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 18:45:57] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 18:46:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 18:46:07] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 18:46:12] Joining segment hits
[2018-10-13 18:48:56] Reporting output tracks
-----------------------------------------------
[2018-10-13 18:52:28] A summary of the alignment counts can be found in /scratch/8793436.1.linga/tophat2/align_summary.txt
[2018-10-13 18:52:28] Run complete: 00:28:08 elapsed