[2018-10-13 02:24:03] Beginning TopHat run (v2.1.1)
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[2018-10-13 02:24:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 02:24:03] Checking for Bowtie index files (genome)..
[2018-10-13 02:24:03] Checking for reference FASTA file
[2018-10-13 02:24:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 02:24:05] Reading known junctions from GTF file
[2018-10-13 02:24:08] Preparing reads
	 left reads: min. length=100, max. length=100, 495913 kept reads (291 discarded)
	right reads: min. length=100, max. length=100, 495495 kept reads (709 discarded)
[2018-10-13 02:24:23] Building transcriptome data files /scratch/8792916.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:24:33] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:29:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:29:43] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:30:10] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:30:10] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:30:33] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:30:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:30:44] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:30:49] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:30:54] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:31:18] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:31:22] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:31:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:31:34] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:31:40] Searching for junctions via segment mapping
[2018-10-13 02:33:05] Retrieving sequences for splices
[2018-10-13 02:34:11] Indexing splices
[2018-10-13 02:34:22] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:34:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:34:27] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:34:29] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:34:32] Joining segment hits
[2018-10-13 02:35:46] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:35:48] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:35:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:35:54] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:35:56] Joining segment hits
[2018-10-13 02:37:11] Reporting output tracks
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[2018-10-13 02:39:11] A summary of the alignment counts can be found in /scratch/8792916.1.p8/tophat2/align_summary.txt
[2018-10-13 02:39:11] Run complete: 00:15:07 elapsed