[2019-06-28 13:25:23] Beginning TopHat run (v2.1.1)
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[2019-06-28 13:25:23] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-28 13:25:24] Checking for Bowtie index files (genome)..
[2019-06-28 13:25:24] Checking for reference FASTA file
[2019-06-28 13:25:24] Generating SAM header for Bowtie2Index/genome
[2019-06-28 13:25:29] Reading known junctions from GTF file
[2019-06-28 13:25:33] Preparing reads
	 left reads: min. length=150, max. length=150, 21922088 kept reads (419 discarded)
	right reads: min. length=150, max. length=150, 21922400 kept reads (107 discarded)
[2019-06-28 13:51:35] Building transcriptome data files /scratch/7287270.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-28 13:51:57] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-28 13:59:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 14:38:52] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-28 15:23:33] Resuming TopHat pipeline with unmapped reads
[2019-06-28 15:23:33] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 16:01:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 16:10:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 16:19:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 16:29:23] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 16:39:10] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 16:45:23] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 16:47:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-28 17:27:19] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-06-28 17:36:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-06-28 17:46:00] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-06-28 17:55:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-06-28 18:05:24] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-06-28 18:13:31] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-06-28 18:17:13] Searching for junctions via segment mapping
[2019-06-29 05:48:09] Retrieving sequences for splices
[2019-06-29 05:51:11] Indexing splices
[2019-06-29 05:53:12] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 06:00:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 06:09:37] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 06:18:17] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 06:27:07] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 06:33:28] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 06:35:14] Joining segment hits
[2019-06-29 06:50:24] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-06-29 06:59:10] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-06-29 07:08:22] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-06-29 07:18:22] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-06-29 07:26:58] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-06-29 07:34:10] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-06-29 07:36:03] Joining segment hits
[2019-06-29 07:52:43] Reporting output tracks
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[2019-06-29 09:49:54] A summary of the alignment counts can be found in /scratch/7287270.1.linga/tophat2/align_summary.txt
[2019-06-29 09:49:54] Run complete: 20:24:30 elapsed