[2019-09-04 11:17:02] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:17:02] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:17:02] Checking for Bowtie index files (genome)..
[2019-09-04 11:17:02] Checking for reference FASTA file
[2019-09-04 11:17:02] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:17:06] Reading known junctions from GTF file
[2019-09-04 11:17:10] Preparing reads
	 left reads: min. length=150, max. length=150, 40105670 kept reads (9 discarded)
	right reads: min. length=150, max. length=150, 40104198 kept reads (1481 discarded)
[2019-09-04 11:57:23] Building transcriptome data files /scratch/9142560.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:57:40] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 12:05:33] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:37:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 13:07:47] Resuming TopHat pipeline with unmapped reads
[2019-09-04 13:07:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 14:02:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 14:09:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 14:18:07] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 14:26:25] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 14:34:35] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 14:41:30] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 14:45:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 15:41:25] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 15:49:33] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:58:19] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 16:07:39] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 16:16:51] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 16:25:03] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 16:30:02] Searching for junctions via segment mapping
[2019-09-04 16:56:42] Retrieving sequences for splices
[2019-09-04 16:58:39] Indexing splices
[2019-09-04 16:59:47] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 17:02:06] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 17:04:24] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 17:06:49] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 17:09:07] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:11:10] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:12:37] Joining segment hits
[2019-09-04 17:21:38] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 17:24:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 17:26:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 17:28:55] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 17:31:31] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:34:08] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:35:57] Joining segment hits
[2019-09-04 17:45:33] Reporting output tracks
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[2019-09-04 18:37:22] A summary of the alignment counts can be found in /scratch/9142560.1.linga/tophat2/align_summary.txt
[2019-09-04 18:37:22] Run complete: 07:20:19 elapsed