[2019-07-05 11:30:29] Beginning TopHat run (v2.1.1)
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[2019-07-05 11:30:29] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 11:30:30] Checking for Bowtie index files (genome)..
[2019-07-05 11:30:30] Checking for reference FASTA file
[2019-07-05 11:30:30] Generating SAM header for Bowtie2Index/genome
[2019-07-05 11:30:32] Reading known junctions from GTF file
[2019-07-05 11:30:34] Preparing reads
	 left reads: min. length=150, max. length=150, 21860722 kept reads (1604 discarded)
	right reads: min. length=150, max. length=150, 21845932 kept reads (16394 discarded)
[2019-07-05 11:49:24] Building transcriptome data files /scratch/7534488.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:49:34] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:53:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:04:05] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 12:15:50] Resuming TopHat pipeline with unmapped reads
[2019-07-05 12:15:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:23:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:23:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:24:23] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:25:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:25:43] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:26:23] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:27:01] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:35:50] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:36:46] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:37:46] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:38:46] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:39:43] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:40:42] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:41:37] Searching for junctions via segment mapping
[2019-07-05 13:19:22] Retrieving sequences for splices
[2019-07-05 13:20:29] Indexing splices
[2019-07-05 13:21:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:21:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:22:03] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:22:30] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:22:58] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:23:25] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:23:49] Joining segment hits
[2019-07-05 13:26:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:26:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:27:24] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:28:03] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:28:42] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:29:19] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:29:53] Joining segment hits
[2019-07-05 13:32:27] Reporting output tracks
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[2019-07-05 14:10:07] A summary of the alignment counts can be found in /scratch/7534488.1.linga/tophat2/align_summary.txt
[2019-07-05 14:10:07] Run complete: 02:39:37 elapsed