[2018-10-13 02:54:08] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:54:08] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:54:08] Checking for Bowtie index files (genome)..
[2018-10-13 02:54:08] Checking for reference FASTA file
[2018-10-13 02:54:08] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:54:11] Reading known junctions from GTF file
[2018-10-13 02:54:13] Preparing reads
	 left reads: min. length=100, max. length=100, 374851 kept reads (199 discarded)
	right reads: min. length=100, max. length=100, 374576 kept reads (474 discarded)
[2018-10-13 02:54:24] Building transcriptome data files /scratch/8792932.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:54:35] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:59:17] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:59:38] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:00:01] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:00:01] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:00:22] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:00:27] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:00:32] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:00:37] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:00:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:01:04] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:01:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:01:15] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:01:20] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:01:25] Searching for junctions via segment mapping
[2018-10-13 03:02:44] Retrieving sequences for splices
[2018-10-13 03:03:51] Indexing splices
[2018-10-13 03:04:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:04:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:04:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:04:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:04:11] Joining segment hits
[2018-10-13 03:05:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:05:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:05:25] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:05:27] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:05:29] Joining segment hits
[2018-10-13 03:06:39] Reporting output tracks
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[2018-10-13 03:08:25] A summary of the alignment counts can be found in /scratch/8792932.1.p16/tophat2/align_summary.txt
[2018-10-13 03:08:25] Run complete: 00:14:16 elapsed