[2018-10-13 05:57:32] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:57:32] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:57:32] Checking for Bowtie index files (genome)..
[2018-10-13 05:57:32] Checking for reference FASTA file
[2018-10-13 05:57:32] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:57:34] Reading known junctions from GTF file
[2018-10-13 05:57:36] Preparing reads
	 left reads: min. length=100, max. length=100, 1245049 kept reads (97 discarded)
	right reads: min. length=100, max. length=100, 1244591 kept reads (555 discarded)
[2018-10-13 05:58:12] Building transcriptome data files /scratch/8793039.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:58:22] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 06:03:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:03:36] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 06:04:08] Resuming TopHat pipeline with unmapped reads
[2018-10-13 06:04:08] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:04:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:04:34] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:04:40] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:04:45] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:04:51] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:05:14] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:05:20] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:05:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:05:33] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:05:39] Searching for junctions via segment mapping
[2018-10-13 06:07:23] Retrieving sequences for splices
[2018-10-13 06:08:31] Indexing splices
[2018-10-13 06:08:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:08:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:08:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:08:50] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:08:52] Joining segment hits
[2018-10-13 06:10:10] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:10:12] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:10:15] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:10:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:10:21] Joining segment hits
[2018-10-13 06:11:39] Reporting output tracks
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[2018-10-13 06:15:21] A summary of the alignment counts can be found in /scratch/8793039.1.p16/tophat2/align_summary.txt
[2018-10-13 06:15:21] Run complete: 00:17:48 elapsed