[2019-09-04 11:15:10] Beginning TopHat run (v2.1.1)
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[2019-09-04 11:15:10] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-09-04 11:15:11] Checking for Bowtie index files (genome)..
[2019-09-04 11:15:11] Checking for reference FASTA file
[2019-09-04 11:15:11] Generating SAM header for Bowtie2Index/genome
[2019-09-04 11:15:13] Reading known junctions from GTF file
[2019-09-04 11:15:16] Preparing reads
	 left reads: min. length=150, max. length=150, 29099147 kept reads (7 discarded)
	right reads: min. length=150, max. length=150, 29098062 kept reads (1092 discarded)
[2019-09-04 11:31:44] Building transcriptome data files /scratch/9142562.1.p16/tophat2/tmp/RefSeq_GeneBody
[2019-09-04 11:31:53] Building Bowtie index from RefSeq_GeneBody.fa
[2019-09-04 11:36:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 11:54:53] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-09-04 12:13:00] Resuming TopHat pipeline with unmapped reads
[2019-09-04 12:13:05] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 12:39:15] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 12:42:35] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 12:46:10] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 12:50:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 12:53:53] Mapping left_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 12:57:11] Mapping left_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 12:59:16] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-09-04 13:26:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/6)
[2019-09-04 13:29:51] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/6)
[2019-09-04 13:33:24] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/6)
[2019-09-04 13:37:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/6)
[2019-09-04 13:40:39] Mapping right_kept_reads.m2g_um_seg5 to genome genome with Bowtie2 (5/6)
[2019-09-04 13:44:07] Mapping right_kept_reads.m2g_um_seg6 to genome genome with Bowtie2 (6/6)
[2019-09-04 13:46:16] Searching for junctions via segment mapping
[2019-09-04 13:55:59] Retrieving sequences for splices
[2019-09-04 13:57:06] Indexing splices
[2019-09-04 13:58:36] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 13:59:21] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 14:00:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 14:00:52] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 14:01:36] Mapping left_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 14:02:16] Mapping left_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 14:02:46] Joining segment hits
[2019-09-04 14:06:07] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/6)
[2019-09-04 14:06:51] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/6)
[2019-09-04 14:07:33] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/6)
[2019-09-04 14:08:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/6)
[2019-09-04 14:09:03] Mapping right_kept_reads.m2g_um_seg5 to genome segment_juncs with Bowtie2 (5/6)
[2019-09-04 14:09:47] Mapping right_kept_reads.m2g_um_seg6 to genome segment_juncs with Bowtie2 (6/6)
[2019-09-04 14:10:21] Joining segment hits
[2019-09-04 14:13:43] Reporting output tracks
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[2019-09-04 14:33:32] A summary of the alignment counts can be found in /scratch/9142562.1.p16/tophat2/align_summary.txt
[2019-09-04 14:33:32] Run complete: 03:18:21 elapsed