[2018-10-13 12:48:31] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:48:31] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:48:31] Checking for Bowtie index files (genome)..
[2018-10-13 12:48:31] Checking for reference FASTA file
[2018-10-13 12:48:31] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:48:33] Reading known junctions from GTF file
[2018-10-13 12:48:35] Preparing reads
	 left reads: min. length=100, max. length=100, 1115665 kept reads (349 discarded)
	right reads: min. length=100, max. length=100, 1115362 kept reads (652 discarded)
[2018-10-13 12:49:09] Building transcriptome data files /scratch/8793243.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:49:20] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:54:40] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:55:32] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:56:23] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:56:24] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:56:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:56:56] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:57:05] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:57:13] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:57:21] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:57:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:57:58] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:58:08] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:58:16] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:58:26] Searching for junctions via segment mapping
[2018-10-13 13:02:26] Retrieving sequences for splices
[2018-10-13 13:03:39] Indexing splices
[2018-10-13 13:03:52] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:03:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:04:00] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:04:05] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:04:09] Joining segment hits
[2018-10-13 13:05:32] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:05:35] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:05:40] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:05:45] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:05:50] Joining segment hits
[2018-10-13 13:07:13] Reporting output tracks
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[2018-10-13 13:17:25] A summary of the alignment counts can be found in /scratch/8793243.1.c/tophat2/align_summary.txt
[2018-10-13 13:17:25] Run complete: 00:28:54 elapsed