[2018-10-13 11:50:56] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:50:56] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:50:56] Checking for Bowtie index files (genome)..
[2018-10-13 11:50:57] Checking for reference FASTA file
[2018-10-13 11:50:57] Generating SAM header for Bowtie2Index/genome
[2018-10-13 11:50:58] Reading known junctions from GTF file
[2018-10-13 11:51:01] Preparing reads
	 left reads: min. length=100, max. length=100, 455673 kept reads (54 discarded)
	right reads: min. length=100, max. length=100, 455564 kept reads (163 discarded)
[2018-10-13 11:51:20] Building transcriptome data files /scratch/8793220.1.c/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 11:51:32] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 11:56:49] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:57:12] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 11:57:36] Resuming TopHat pipeline with unmapped reads
[2018-10-13 11:57:36] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:57:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:57:52] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:57:58] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:58:02] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:58:07] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 11:58:23] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 11:58:28] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 11:58:35] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 11:58:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 11:58:46] Searching for junctions via segment mapping
[2018-10-13 12:00:45] Retrieving sequences for splices
[2018-10-13 12:01:58] Indexing splices
[2018-10-13 12:02:10] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:02:12] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:02:15] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:02:18] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:02:21] Joining segment hits
[2018-10-13 12:03:41] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 12:03:44] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 12:03:47] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 12:03:50] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 12:03:53] Joining segment hits
[2018-10-13 12:05:14] Reporting output tracks
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[2018-10-13 12:08:13] A summary of the alignment counts can be found in /scratch/8793220.1.c/tophat2/align_summary.txt
[2018-10-13 12:08:13] Run complete: 00:17:16 elapsed