[2019-09-04 11:15:29] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:15:29] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:15:30] Checking for Bowtie index files (genome)..
[2019-09-04 11:15:30] Checking for reference FASTA file
[2019-09-04 11:15:30] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:15:31] Reading known junctions from GTF file
[2019-09-04 11:15:34] Preparing reads
	 left reads: min. length=150, max. length=150, 34143243 kept reads (6 discarded)
	right reads: min. length=150, max. length=150, 34141944 kept reads (1305 discarded)
[2019-09-04 11:35:15] Building transcriptome data files /scratch/9142564.1.c/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:35:24] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:40:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:56:41] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 14:06:39] Resuming TopHat pipeline with unmapped reads
[2019-09-04 14:06:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 14:55:13] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 15:02:17] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 15:09:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 15:16:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 15:23:45] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 15:29:28] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 15:32:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 16:17:47] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 16:23:42] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 16:30:28] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 16:37:17] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 16:44:05] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 16:50:10] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 16:53:45] Searching for junctions via segment mapping
[2019-09-04 17:04:56] Retrieving sequences for splices
[2019-09-04 17:06:02] Indexing splices
[2019-09-04 17:06:37] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 17:08:47] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 17:10:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 17:13:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 17:15:17] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:17:04] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:18:03] Joining segment hits
[2019-09-04 17:23:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 17:24:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 17:26:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 17:27:35] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 17:29:22] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 17:31:02] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 17:32:25] Joining segment hits
[2019-09-04 17:37:51] Reporting output tracks
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[2019-09-04 18:07:02] A summary of the alignment counts can be found in /scratch/9142564.1.c/tophat2/align_summary.txt
[2019-09-04 18:07:02] Run complete: 06:51:32 elapsed