[2018-10-13 14:04:32] Beginning TopHat run (v2.1.1)
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[2018-10-13 14:04:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 14:04:32] Checking for Bowtie index files (genome)..
[2018-10-13 14:04:32] Checking for reference FASTA file
[2018-10-13 14:04:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 14:04:34] Reading known junctions from GTF file
[2018-10-13 14:04:36] Preparing reads
	 left reads: min. length=100, max. length=100, 1126436 kept reads (210 discarded)
	right reads: min. length=100, max. length=100, 1126148 kept reads (498 discarded)
[2018-10-13 14:05:08] Building transcriptome data files /scratch/8793280.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 14:05:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 14:10:37] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:11:24] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 14:12:11] Resuming TopHat pipeline with unmapped reads
[2018-10-13 14:12:11] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:12:41] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:12:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:12:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:13:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:13:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 14:13:41] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 14:13:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 14:13:56] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 14:14:03] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 14:14:11] Searching for junctions via segment mapping
[2018-10-13 14:17:18] Retrieving sequences for splices
[2018-10-13 14:18:31] Indexing splices
[2018-10-13 14:18:43] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:18:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:18:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:18:54] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:18:58] Joining segment hits
[2018-10-13 14:20:21] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 14:20:25] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 14:20:28] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 14:20:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 14:20:36] Joining segment hits
[2018-10-13 14:22:00] Reporting output tracks
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[2018-10-13 14:31:16] A summary of the alignment counts can be found in /scratch/8793280.1.c/tophat2/align_summary.txt
[2018-10-13 14:31:16] Run complete: 00:26:43 elapsed