[2018-10-13 04:04:54] Beginning TopHat run (v2.1.1)
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[2018-10-13 04:04:54] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 04:04:54] Checking for Bowtie index files (genome)..
[2018-10-13 04:04:54] Checking for reference FASTA file
[2018-10-13 04:04:54] Generating SAM header for Bowtie2Index/genome
[2018-10-13 04:04:58] Reading known junctions from GTF file
[2018-10-13 04:05:03] Preparing reads
	 left reads: min. length=100, max. length=100, 682186 kept reads (121 discarded)
	right reads: min. length=100, max. length=100, 682069 kept reads (238 discarded)
[2018-10-13 04:05:31] Building transcriptome data files /scratch/8792982.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 04:05:50] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 04:14:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:14:39] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 04:15:16] Resuming TopHat pipeline with unmapped reads
[2018-10-13 04:15:16] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:15:38] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:15:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:15:56] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:16:05] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:16:15] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 04:16:39] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 04:16:47] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 04:16:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 04:17:07] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 04:17:16] Searching for junctions via segment mapping
[2018-10-13 04:20:44] Retrieving sequences for splices
[2018-10-13 04:23:05] Indexing splices
[2018-10-13 04:23:26] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:23:31] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:23:36] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:23:42] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:23:47] Joining segment hits
[2018-10-13 04:26:17] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 04:26:22] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 04:26:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 04:26:32] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 04:26:38] Joining segment hits
[2018-10-13 04:29:12] Reporting output tracks
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[2018-10-13 04:35:15] A summary of the alignment counts can be found in /scratch/8792982.1.linga/tophat2/align_summary.txt
[2018-10-13 04:35:15] Run complete: 00:30:21 elapsed