[2018-10-13 06:03:07] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 06:03:07] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 06:03:07] Checking for Bowtie index files (genome)..
[2018-10-13 06:03:07] Checking for reference FASTA file
[2018-10-13 06:03:07] Generating SAM header for Bowtie2Index/genome
[2018-10-13 06:03:12] Reading known junctions from GTF file
[2018-10-13 06:03:17] Preparing reads
	 left reads: min. length=100, max. length=100, 646597 kept reads (56 discarded)
	right reads: min. length=100, max. length=100, 646440 kept reads (213 discarded)
[2018-10-13 06:03:47] Building transcriptome data files /scratch/8793041.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 06:04:07] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:13:00] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:13:59] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:14:59] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:14:59] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:15:25] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:15:33] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:15:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:15:55] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:16:06] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:16:36] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:16:45] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:16:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:17:10] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:17:21] Searching for junctions via segment mapping
[2018-10-13 06:22:39] Retrieving sequences for splices
[2018-10-13 06:24:50] Indexing splices
[2018-10-13 06:25:13] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:25:19] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:25:26] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:25:33] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:25:41] Joining segment hits
[2018-10-13 06:28:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:28:16] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:28:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:28:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:28:39] Joining segment hits
[2018-10-13 06:31:18] Reporting output tracks
-----------------------------------------------
[2018-10-13 06:44:03] A summary of the alignment counts can be found in /scratch/8793041.1.linga/tophat2/align_summary.txt
[2018-10-13 06:44:03] Run complete: 00:40:55 elapsed