[2019-06-26 15:38:01] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-06-26 15:38:01] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 15:38:01] Checking for Bowtie index files (genome)..
[2019-06-26 15:38:01] Checking for reference FASTA file
[2019-06-26 15:38:01] Generating SAM header for Bowtie2Index/genome
[2019-06-26 15:38:11] Reading known junctions from GTF file
[2019-06-26 15:38:15] Preparing reads
	 left reads: min. length=35, max. length=76, 22709381 kept reads (1896804 discarded)
	right reads: min. length=35, max. length=76, 24197601 kept reads (408584 discarded)
[2019-06-26 15:55:03] Building transcriptome data files /scratch/7076172.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 15:55:24] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 16:02:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 16:25:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 17:08:06] Resuming TopHat pipeline with unmapped reads
[2019-06-26 17:08:06] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 17:22:37] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 17:26:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 17:29:53] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 17:33:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 18:04:40] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 18:14:34] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 18:24:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 18:34:47] Searching for junctions via segment mapping
[2019-06-26 18:45:50] Retrieving sequences for splices
[2019-06-26 18:48:16] Indexing splices
[2019-06-26 18:48:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 18:48:53] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 18:51:54] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 18:54:30] Joining segment hits
[2019-06-26 18:59:09] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 18:59:30] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 19:06:16] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 19:13:57] Joining segment hits
[2019-06-26 19:22:30] Reporting output tracks
-----------------------------------------------
[2019-06-26 21:32:50] A summary of the alignment counts can be found in /scratch/7076172.1.linga/tophat2/align_summary.txt
[2019-06-26 21:32:50] Run complete: 05:54:48 elapsed