[2019-06-26 15:02:46] Beginning TopHat run (v2.1.1)
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[2019-06-26 15:02:46] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 15:02:46] Checking for Bowtie index files (genome)..
[2019-06-26 15:02:46] Checking for reference FASTA file
[2019-06-26 15:02:46] Generating SAM header for Bowtie2Index/genome
[2019-06-26 15:02:47] Reading known junctions from GTF file
[2019-06-26 15:02:49] Preparing reads
	 left reads: min. length=35, max. length=76, 25975935 kept reads (705015 discarded)
	right reads: min. length=35, max. length=76, 26543786 kept reads (137164 discarded)
[2019-06-26 15:12:52] Building transcriptome data files /scratch/7076171.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 15:13:01] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 15:17:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 15:27:49] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 15:39:28] Resuming TopHat pipeline with unmapped reads
[2019-06-26 15:39:28] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 15:44:49] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 15:46:05] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 15:47:25] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 15:48:52] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 15:55:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 15:57:21] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 15:59:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 16:01:09] Searching for junctions via segment mapping
[2019-06-26 16:04:26] Retrieving sequences for splices
[2019-06-26 16:05:35] Indexing splices
[2019-06-26 16:05:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 16:05:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 16:06:21] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 16:06:59] Joining segment hits
[2019-06-26 16:08:43] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 16:08:54] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 16:09:26] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 16:10:17] Joining segment hits
[2019-06-26 16:12:07] Reporting output tracks
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[2019-06-26 17:18:45] A summary of the alignment counts can be found in /scratch/7076171.1.p8/tophat2/align_summary.txt
[2019-06-26 17:18:45] Run complete: 02:15:58 elapsed