[2018-10-13 05:05:16] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:05:16] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:05:16] Checking for Bowtie index files (genome)..
[2018-10-13 05:05:16] Checking for reference FASTA file
[2018-10-13 05:05:16] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:05:18] Reading known junctions from GTF file
[2018-10-13 05:05:20] Preparing reads
	 left reads: min. length=100, max. length=100, 1078468 kept reads (145 discarded)
	right reads: min. length=100, max. length=100, 1078247 kept reads (366 discarded)
[2018-10-13 05:05:48] Building transcriptome data files /scratch/8793014.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:06:01] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:10:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:12:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:13:39] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:13:39] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:14:00] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:14:06] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:14:15] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:14:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:14:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 05:14:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 05:14:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 05:15:05] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 05:15:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 05:15:21] Searching for junctions via segment mapping
[2018-10-13 05:22:45] Retrieving sequences for splices
[2018-10-13 05:23:52] Indexing splices
[2018-10-13 05:24:06] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:24:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:24:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:24:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:24:37] Joining segment hits
[2018-10-13 05:25:55] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 05:25:59] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 05:26:08] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 05:26:17] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 05:26:25] Joining segment hits
[2018-10-13 05:27:43] Reporting output tracks
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[2018-10-13 05:52:39] A summary of the alignment counts can be found in /scratch/8793014.1.p16/tophat2/align_summary.txt
[2018-10-13 05:52:39] Run complete: 00:47:23 elapsed