[2018-10-13 16:35:37] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 16:35:37] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:35:37] Checking for Bowtie index files (genome)..
[2018-10-13 16:35:37] Checking for reference FASTA file
[2018-10-13 16:35:37] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:35:43] Reading known junctions from GTF file
[2018-10-13 16:35:55] Preparing reads
	 left reads: min. length=100, max. length=100, 102445 kept reads (93 discarded)
	right reads: min. length=100, max. length=100, 102256 kept reads (282 discarded)
[2018-10-13 16:36:04] Building transcriptome data files /scratch/8793364.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:36:30] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:45:14] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:45:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:45:44] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:45:44] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:45:59] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:46:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:46:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:46:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:46:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:46:45] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:46:52] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:47:01] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:47:08] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:47:16] Searching for junctions via segment mapping
[2018-10-13 16:49:42] Retrieving sequences for splices
[2018-10-13 16:51:53] Indexing splices
[2018-10-13 16:52:14] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:52:17] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:52:22] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:52:25] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:52:30] Joining segment hits
[2018-10-13 16:54:35] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:54:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:54:43] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:54:47] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:54:52] Joining segment hits
[2018-10-13 16:57:03] Reporting output tracks
-----------------------------------------------
[2018-10-13 16:59:24] A summary of the alignment counts can be found in /scratch/8793364.1.linga/tophat2/align_summary.txt
[2018-10-13 16:59:24] Run complete: 00:23:47 elapsed