[2018-10-13 03:14:58] Beginning TopHat run (v2.1.1)
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[2018-10-13 03:14:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 03:14:58] Checking for Bowtie index files (genome)..
[2018-10-13 03:14:58] Checking for reference FASTA file
[2018-10-13 03:14:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 03:15:02] Reading known junctions from GTF file
[2018-10-13 03:15:07] Preparing reads
	 left reads: min. length=100, max. length=100, 280600 kept reads (212 discarded)
	right reads: min. length=100, max. length=100, 280362 kept reads (450 discarded)
[2018-10-13 03:15:19] Building transcriptome data files /scratch/8792948.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 03:15:39] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 03:24:35] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:25:09] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 03:25:45] Resuming TopHat pipeline with unmapped reads
[2018-10-13 03:25:45] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:26:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:26:38] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:26:52] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:27:03] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:27:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 03:27:57] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 03:28:09] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 03:28:23] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 03:28:36] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 03:28:48] Searching for junctions via segment mapping
[2018-10-13 03:31:23] Retrieving sequences for splices
[2018-10-13 03:33:34] Indexing splices
[2018-10-13 03:33:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:33:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:34:02] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:34:07] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:34:11] Joining segment hits
[2018-10-13 03:36:36] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 03:36:41] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 03:36:46] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 03:36:51] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 03:36:55] Joining segment hits
[2018-10-13 03:39:23] Reporting output tracks
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[2018-10-13 03:42:42] A summary of the alignment counts can be found in /scratch/8792948.1.linga/tophat2/align_summary.txt
[2018-10-13 03:42:42] Run complete: 00:27:44 elapsed