[2018-10-13 03:00:26] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 03:00:26] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:00:26] Checking for Bowtie index files (genome)..
[2018-10-13 03:00:26] Checking for reference FASTA file
[2018-10-13 03:00:26] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:00:31] Reading known junctions from GTF file
[2018-10-13 03:00:35] Preparing reads
	 left reads: min. length=100, max. length=100, 671814 kept reads (429 discarded)
	right reads: min. length=100, max. length=100, 671376 kept reads (867 discarded)
[2018-10-13 03:01:04] Building transcriptome data files /scratch/8792940.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:01:23] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:09:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:10:13] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:11:09] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:11:09] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:12:04] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:12:15] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:12:31] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:12:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:12:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:13:52] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:14:04] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:14:22] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:14:35] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:14:47] Searching for junctions via segment mapping
[2018-10-13 03:17:48] Retrieving sequences for splices
[2018-10-13 03:20:01] Indexing splices
[2018-10-13 03:20:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:20:26] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:20:32] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:20:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:20:41] Joining segment hits
[2018-10-13 03:23:14] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:23:19] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:23:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:23:30] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:23:35] Joining segment hits
[2018-10-13 03:26:07] Reporting output tracks
-----------------------------------------------
[2018-10-13 03:30:57] A summary of the alignment counts can be found in /scratch/8792940.1.linga/tophat2/align_summary.txt
[2018-10-13 03:30:57] Run complete: 00:30:30 elapsed