[2019-06-19 17:18:11] Beginning TopHat run (v2.1.1)
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[2019-06-19 17:18:11] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-19 17:18:11] Checking for Bowtie index files (genome)..
[2019-06-19 17:18:11] Checking for reference FASTA file
[2019-06-19 17:18:11] Generating SAM header for Bowtie2Index/genome
[2019-06-19 17:18:17] Reading known junctions from GTF file
[2019-06-19 17:18:21] Preparing reads
	 left reads: min. length=150, max. length=150, 22394727 kept reads (731 discarded)
	right reads: min. length=150, max. length=150, 22392941 kept reads (2517 discarded)
[2019-06-19 17:47:52] Building transcriptome data files /scratch/6873226.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-19 17:48:11] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-19 17:55:23] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-19 18:13:56] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-19 18:34:06] Resuming TopHat pipeline with unmapped reads
[2019-06-19 18:34:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-19 19:03:50] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-19 19:07:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-19 19:10:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-19 19:14:42] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-19 19:18:26] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-19 19:21:23] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-19 19:22:55] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-19 20:05:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-19 20:11:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-19 20:15:59] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-19 20:20:55] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-19 20:25:49] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-19 20:29:59] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-19 20:32:52] Searching for junctions via segment mapping
[2019-06-19 22:49:47] Retrieving sequences for splices
[2019-06-19 22:52:10] Indexing splices
[2019-06-19 22:52:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-19 22:54:55] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-19 22:57:08] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-19 22:59:16] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-19 23:01:23] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-19 23:02:57] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-19 23:03:29] Joining segment hits
[2019-06-19 23:10:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-19 23:13:18] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-19 23:16:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-19 23:18:46] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-19 23:21:20] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-19 23:23:13] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-19 23:24:03] Joining segment hits
[2019-06-19 23:31:57] Reporting output tracks
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[2019-06-20 00:21:43] A summary of the alignment counts can be found in /scratch/6873226.1.linga/tophat2/align_summary.txt
[2019-06-20 00:21:43] Run complete: 07:03:31 elapsed