[2019-06-24 17:43:58] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2019-06-24 17:43:58] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-24 17:43:58] Checking for Bowtie index files (genome)..
[2019-06-24 17:43:58] Checking for reference FASTA file
[2019-06-24 17:43:58] Generating SAM header for Bowtie2Index/genome
[2019-06-24 17:44:00] Reading known junctions from GTF file
[2019-06-24 17:44:03] Preparing reads
	 left reads: min. length=101, max. length=101, 41848119 kept reads (3499 discarded)
	right reads: min. length=101, max. length=101, 41828680 kept reads (22938 discarded)
[2019-06-24 18:27:49] Building transcriptome data files /scratch/7056783.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-24 18:28:06] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-24 18:34:03] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:06:14] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-24 19:39:13] Resuming TopHat pipeline with unmapped reads
[2019-06-24 19:39:14] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 19:59:24] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:02:44] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:06:26] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:10:07] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:13:18] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-24 20:32:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-06-24 20:36:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-06-24 20:40:48] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-06-24 20:44:51] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-06-24 20:48:56] Searching for junctions via segment mapping
[2019-06-24 21:44:49] Retrieving sequences for splices
[2019-06-24 21:47:03] Indexing splices
[2019-06-24 21:48:39] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 21:50:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 21:52:55] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 21:55:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 21:56:56] Joining segment hits
[2019-06-24 22:03:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-06-24 22:05:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-06-24 22:08:18] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-06-24 22:10:41] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-06-24 22:12:42] Joining segment hits
[2019-06-24 22:19:47] Reporting output tracks
-----------------------------------------------
[2019-06-25 00:46:28] A summary of the alignment counts can be found in /scratch/7056783.1.linga/tophat2/align_summary.txt
[2019-06-25 00:46:28] Run complete: 07:02:30 elapsed