[2019-07-12 13:52:13] Beginning TopHat run (v2.1.1)
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[2019-07-12 13:52:13] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-07-12 13:52:13] Checking for Bowtie index files (genome)..
[2019-07-12 13:52:13] Checking for reference FASTA file
[2019-07-12 13:52:13] Generating SAM header for Bowtie2Index/genome
[2019-07-12 13:52:18] Reading known junctions from GTF file
[2019-07-12 13:52:22] Preparing reads
	 left reads: min. length=151, max. length=151, 63385635 kept reads (4382 discarded)
	right reads: min. length=151, max. length=151, 63374806 kept reads (15211 discarded)
[2019-07-12 15:05:24] Building transcriptome data files /scratch/7678201.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-07-12 15:05:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-07-12 15:12:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 17:07:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-07-12 18:47:05] Resuming TopHat pipeline with unmapped reads
[2019-07-12 18:47:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-12 22:10:01] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-12 22:58:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-12 23:48:54] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 00:40:08] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 01:21:46] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 01:54:01] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 02:10:39] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-07-13 05:45:46] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-07-13 06:31:57] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-07-13 07:15:38] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-07-13 08:03:29] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-07-13 08:49:57] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-07-13 09:24:26] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-07-13 09:43:50] Searching for junctions via segment mapping
[2019-07-15 06:09:03] Retrieving sequences for splices
[2019-07-15 06:11:11] Indexing splices
[2019-07-15 06:13:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-15 06:55:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-15 07:36:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-15 08:17:47] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-15 08:57:13] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-15 09:26:21] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-15 09:34:24] Joining segment hits
[2019-07-15 10:31:59] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-07-15 11:16:03] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-07-15 11:59:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-07-15 12:43:06] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-07-15 13:24:47] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-07-15 13:55:14] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-07-15 14:04:49] Joining segment hits
[2019-07-15 15:13:36] Reporting output tracks
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[2019-07-15 19:03:56] A summary of the alignment counts can be found in /scratch/7678201.1.linga/tophat2/align_summary.txt
[2019-07-15 19:03:56] Run complete: 3 days 05:11:42 elapsed