[2018-10-12 23:12:35] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-12 23:12:35] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:12:35] Checking for Bowtie index files (genome)..
[2018-10-12 23:12:35] Checking for reference FASTA file
[2018-10-12 23:12:35] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:12:42] Reading known junctions from GTF file
[2018-10-12 23:12:49] Preparing reads
	 left reads: min. length=100, max. length=100, 453646 kept reads (273 discarded)
	right reads: min. length=100, max. length=100, 453293 kept reads (626 discarded)
[2018-10-12 23:13:17] Building transcriptome data files /scratch/8792828.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:13:39] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:24:28] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:25:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:26:29] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:26:29] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:27:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:27:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:28:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:28:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:28:35] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:29:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:30:01] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:30:26] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:30:44] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:31:01] Searching for junctions via segment mapping
[2018-10-12 23:34:36] Retrieving sequences for splices
[2018-10-12 23:37:29] Indexing splices
[2018-10-12 23:37:58] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:38:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:38:14] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:38:21] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:38:28] Joining segment hits
[2018-10-12 23:42:19] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:42:26] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:43:21] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:44:05] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:44:12] Joining segment hits
[2018-10-12 23:47:06] Reporting output tracks
-----------------------------------------------
[2018-10-12 23:51:30] A summary of the alignment counts can be found in /scratch/8792828.1.linga/tophat2/align_summary.txt
[2018-10-12 23:51:30] Run complete: 00:38:54 elapsed