[2018-10-13 11:25:09] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:25:09] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:25:09] Checking for Bowtie index files (genome)..
[2018-10-13 11:25:09] Checking for reference FASTA file
[2018-10-13 11:25:09] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:25:11] Reading known junctions from GTF file
[2018-10-13 11:25:14] Preparing reads
	 left reads: min. length=100, max. length=100, 1139236 kept reads (160 discarded)
	right reads: min. length=100, max. length=100, 1138938 kept reads (458 discarded)
[2018-10-13 11:25:47] Building transcriptome data files /scratch/8793204.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:25:58] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:31:30] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:32:07] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:32:45] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:32:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:33:06] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:33:11] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:33:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:33:24] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:33:30] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:33:55] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:34:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:34:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:34:15] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:34:22] Searching for junctions via segment mapping
[2018-10-13 11:36:44] Retrieving sequences for splices
[2018-10-13 11:37:57] Indexing splices
[2018-10-13 11:38:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:38:13] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:38:17] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:38:20] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:38:24] Joining segment hits
[2018-10-13 11:39:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 11:39:50] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 11:39:54] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 11:39:57] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 11:40:01] Joining segment hits
[2018-10-13 11:41:25] Reporting output tracks
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[2018-10-13 11:47:25] A summary of the alignment counts can be found in /scratch/8793204.1.c/tophat2/align_summary.txt
[2018-10-13 11:47:25] Run complete: 00:22:15 elapsed