[2018-10-13 13:42:34] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 13:42:34] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 13:42:34] Checking for Bowtie index files (genome)..
[2018-10-13 13:42:34] Checking for reference FASTA file
[2018-10-13 13:42:34] Generating SAM header for Bowtie2Index/genome
[2018-10-13 13:42:39] Reading known junctions from GTF file
[2018-10-13 13:42:43] Preparing reads
	 left reads: min. length=100, max. length=100, 1314744 kept reads (88 discarded)
	right reads: min. length=100, max. length=100, 1314325 kept reads (507 discarded)
[2018-10-13 13:43:37] Building transcriptome data files /scratch/8793269.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 13:43:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 13:51:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:52:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 13:54:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 13:54:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:54:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:55:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:55:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:55:33] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:55:44] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 13:56:29] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 13:56:39] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 13:56:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 13:57:07] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 13:57:19] Searching for junctions via segment mapping
[2018-10-13 14:01:37] Retrieving sequences for splices
[2018-10-13 14:03:46] Indexing splices
[2018-10-13 14:04:07] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:04:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:04:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:04:25] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:04:31] Joining segment hits
[2018-10-13 14:06:58] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:07:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:07:11] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:07:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:07:24] Joining segment hits
[2018-10-13 14:09:48] Reporting output tracks
-----------------------------------------------
[2018-10-13 14:21:30] A summary of the alignment counts can be found in /scratch/8793269.1.linga/tophat2/align_summary.txt
[2018-10-13 14:21:30] Run complete: 00:38:56 elapsed