[2018-10-13 09:44:58] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 09:44:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 09:44:58] Checking for Bowtie index files (genome)..
[2018-10-13 09:44:58] Checking for reference FASTA file
[2018-10-13 09:44:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 09:45:02] Reading known junctions from GTF file
[2018-10-13 09:45:06] Preparing reads
	 left reads: min. length=100, max. length=100, 1496930 kept reads (152 discarded)
	right reads: min. length=100, max. length=100, 1496446 kept reads (636 discarded)
[2018-10-13 09:46:06] Building transcriptome data files /scratch/8793153.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 09:46:24] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 09:54:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:55:19] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 09:56:31] Resuming TopHat pipeline with unmapped reads
[2018-10-13 09:56:31] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:57:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:57:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:57:41] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:57:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:58:05] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 09:58:53] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 09:59:03] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 09:59:21] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 09:59:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 09:59:47] Searching for junctions via segment mapping
[2018-10-13 10:03:58] Retrieving sequences for splices
[2018-10-13 10:06:05] Indexing splices
[2018-10-13 10:06:28] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:06:34] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:06:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:06:48] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:06:55] Joining segment hits
[2018-10-13 10:09:27] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 10:09:34] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 10:09:42] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 10:09:49] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 10:09:56] Joining segment hits
[2018-10-13 10:12:33] Reporting output tracks
-----------------------------------------------
[2018-10-13 10:26:20] A summary of the alignment counts can be found in /scratch/8793153.1.linga/tophat2/align_summary.txt
[2018-10-13 10:26:20] Run complete: 00:41:21 elapsed