[2018-10-13 05:53:15] Beginning TopHat run (v2.1.1)
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[2018-10-13 05:53:15] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 05:53:15] Checking for Bowtie index files (genome)..
[2018-10-13 05:53:15] Checking for reference FASTA file
[2018-10-13 05:53:15] Generating SAM header for Bowtie2Index/genome
[2018-10-13 05:53:17] Reading known junctions from GTF file
[2018-10-13 05:53:20] Preparing reads
	 left reads: min. length=100, max. length=100, 1114905 kept reads (75 discarded)
	right reads: min. length=100, max. length=100, 1114645 kept reads (335 discarded)
[2018-10-13 05:53:52] Building transcriptome data files /scratch/8793036.1.p8/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 05:54:02] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 05:58:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:59:17] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 05:59:50] Resuming TopHat pipeline with unmapped reads
[2018-10-13 05:59:50] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:00:11] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:00:16] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:00:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:00:27] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:00:33] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 06:00:55] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 06:01:00] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 06:01:07] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 06:01:13] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 06:01:19] Searching for junctions via segment mapping
[2018-10-13 06:03:15] Retrieving sequences for splices
[2018-10-13 06:04:21] Indexing splices
[2018-10-13 06:04:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:04:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:04:39] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:04:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:04:44] Joining segment hits
[2018-10-13 06:06:01] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 06:06:04] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 06:06:07] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 06:06:09] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 06:06:12] Joining segment hits
[2018-10-13 06:07:29] Reporting output tracks
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[2018-10-13 06:12:20] A summary of the alignment counts can be found in /scratch/8793036.1.p8/tophat2/align_summary.txt
[2018-10-13 06:12:20] Run complete: 00:19:05 elapsed