[2018-10-13 03:56:10] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:56:10] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:56:10] Checking for Bowtie index files (genome)..
[2018-10-13 03:56:10] Checking for reference FASTA file
[2018-10-13 03:56:10] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:56:12] Reading known junctions from GTF file
[2018-10-13 03:56:14] Preparing reads
	 left reads: min. length=100, max. length=100, 184523 kept reads (124 discarded)
	right reads: min. length=100, max. length=100, 184370 kept reads (277 discarded)
[2018-10-13 03:56:20] Building transcriptome data files /scratch/8792979.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:56:29] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:01:18] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:01:30] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:01:43] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:01:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:01:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:01:58] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:02:02] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:02:06] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:02:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:02:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:02:25] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:02:30] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:02:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:02:38] Searching for junctions via segment mapping
[2018-10-13 04:03:57] Retrieving sequences for splices
[2018-10-13 04:05:04] Indexing splices
[2018-10-13 04:05:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:05:18] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:05:20] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:05:22] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:05:24] Joining segment hits
[2018-10-13 04:06:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:06:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:06:37] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:06:39] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:06:42] Joining segment hits
[2018-10-13 04:07:51] Reporting output tracks
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[2018-10-13 04:09:34] A summary of the alignment counts can be found in /scratch/8792979.1.p16/tophat2/align_summary.txt
[2018-10-13 04:09:34] Run complete: 00:13:24 elapsed