[2018-10-13 09:13:28] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 09:13:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:13:28] Checking for Bowtie index files (genome)..
[2018-10-13 09:13:28] Checking for reference FASTA file
[2018-10-13 09:13:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:13:32] Reading known junctions from GTF file
[2018-10-13 09:13:36] Preparing reads
	 left reads: min. length=100, max. length=100, 1504885 kept reads (102 discarded)
	right reads: min. length=100, max. length=100, 1504400 kept reads (587 discarded)
[2018-10-13 09:14:37] Building transcriptome data files /scratch/8793142.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:14:56] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:22:57] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:24:01] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:25:05] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:25:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:25:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:25:50] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:26:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:26:14] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:26:24] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:27:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:27:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:27:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:27:43] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:27:55] Searching for junctions via segment mapping
[2018-10-13 09:32:06] Retrieving sequences for splices
[2018-10-13 09:34:06] Indexing splices
[2018-10-13 09:34:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:34:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:34:38] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:34:44] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:34:50] Joining segment hits
[2018-10-13 09:37:37] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 09:37:43] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 09:37:50] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 09:37:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 09:38:03] Joining segment hits
[2018-10-13 09:41:14] Reporting output tracks
-----------------------------------------------
[2018-10-13 09:52:45] A summary of the alignment counts can be found in /scratch/8793142.1.linga/tophat2/align_summary.txt
[2018-10-13 09:52:45] Run complete: 00:39:17 elapsed