[2019-07-04 02:12:33] Beginning TopHat run (v2.1.1)
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[2019-07-04 02:12:33] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-04 02:12:33] Checking for Bowtie index files (genome)..
[2019-07-04 02:12:33] Checking for reference FASTA file
[2019-07-04 02:12:33] Generating SAM header for Bowtie2Index/genome
[2019-07-04 02:12:36] Reading known junctions from GTF file
[2019-07-04 02:12:40] Preparing reads
	 left reads: min. length=150, max. length=150, 32341251 kept reads (459 discarded)
	right reads: min. length=150, max. length=150, 32341627 kept reads (83 discarded)
[2019-07-04 02:54:36] Building transcriptome data files /scratch/7505712.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-04 02:54:57] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-04 03:03:09] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 03:27:54] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-04 03:52:57] Resuming TopHat pipeline with unmapped reads
[2019-07-04 03:52:57] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 05:24:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 05:36:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 05:48:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 05:59:47] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 06:11:42] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 06:19:01] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 06:22:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-04 07:51:28] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-04 08:04:50] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-04 08:16:09] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-04 08:28:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-04 08:39:48] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-04 08:48:36] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-04 08:53:01] Searching for junctions via segment mapping
[2019-07-04 15:22:49] Retrieving sequences for splices
[2019-07-04 15:25:14] Indexing splices
[2019-07-04 15:26:17] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 15:33:40] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 15:41:09] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 15:49:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 15:56:40] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 16:01:16] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 16:02:31] Joining segment hits
[2019-07-04 16:17:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-04 16:25:20] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-04 16:33:02] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-04 16:40:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-04 16:48:03] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-04 16:52:30] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-04 16:53:54] Joining segment hits
[2019-07-04 17:09:10] Reporting output tracks
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[2019-07-04 18:04:20] A summary of the alignment counts can be found in /scratch/7505712.1.linga/tophat2/align_summary.txt
[2019-07-04 18:04:20] Run complete: 15:51:47 elapsed