[2019-07-05 10:57:28] Beginning TopHat run (v2.1.1)
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[2019-07-05 10:57:28] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-05 10:57:28] Checking for Bowtie index files (genome)..
[2019-07-05 10:57:28] Checking for reference FASTA file
[2019-07-05 10:57:28] Generating SAM header for Bowtie2Index/genome
[2019-07-05 10:57:31] Reading known junctions from GTF file
[2019-07-05 10:57:34] Preparing reads
	 left reads: min. length=150, max. length=150, 21134222 kept reads (1698 discarded)
	right reads: min. length=150, max. length=150, 21121472 kept reads (14448 discarded)
[2019-07-05 11:15:11] Building transcriptome data files /scratch/7534469.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-05 11:15:20] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-05 11:18:52] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:31:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-05 11:45:51] Resuming TopHat pipeline with unmapped reads
[2019-07-05 11:45:51] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 11:53:39] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 11:54:21] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 11:55:04] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 11:55:53] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 11:56:43] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 11:57:27] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 11:58:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-05 12:06:58] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-05 12:08:05] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-05 12:09:13] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-05 12:10:26] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-05 12:11:39] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-05 12:12:44] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-05 12:13:48] Searching for junctions via segment mapping
[2019-07-05 13:24:28] Retrieving sequences for splices
[2019-07-05 13:25:35] Indexing splices
[2019-07-05 13:26:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:27:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:28:04] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:28:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:29:34] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:30:17] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:30:56] Joining segment hits
[2019-07-05 13:33:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-05 13:36:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-05 13:38:03] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-05 13:40:01] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-05 13:41:55] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-05 13:43:33] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-05 13:45:09] Joining segment hits
[2019-07-05 13:48:31] Reporting output tracks
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[2019-07-05 14:37:09] A summary of the alignment counts can be found in /scratch/7534469.1.linga/tophat2/align_summary.txt
[2019-07-05 14:37:09] Run complete: 03:39:40 elapsed