[2018-10-13 01:59:29] Beginning TopHat run (v2.1.1)
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[2018-10-13 01:59:29] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 01:59:29] Checking for Bowtie index files (genome)..
[2018-10-13 01:59:29] Checking for reference FASTA file
[2018-10-13 01:59:29] Generating SAM header for Bowtie2Index/genome
[2018-10-13 01:59:34] Reading known junctions from GTF file
[2018-10-13 01:59:38] Preparing reads
	 left reads: min. length=100, max. length=100, 325143 kept reads (169 discarded)
	right reads: min. length=100, max. length=100, 324839 kept reads (473 discarded)
[2018-10-13 01:59:53] Building transcriptome data files /scratch/8792902.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 02:00:12] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 02:08:19] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:08:50] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 02:09:21] Resuming TopHat pipeline with unmapped reads
[2018-10-13 02:09:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:09:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:10:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:10:13] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:10:22] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:10:32] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 02:11:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 02:11:15] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 02:11:27] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 02:11:37] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 02:11:46] Searching for junctions via segment mapping
[2018-10-13 02:14:25] Retrieving sequences for splices
[2018-10-13 02:16:28] Indexing splices
[2018-10-13 02:16:49] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:16:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:16:58] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:17:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:17:07] Joining segment hits
[2018-10-13 02:19:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 02:19:23] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 02:19:27] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 02:19:31] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 02:19:35] Joining segment hits
[2018-10-13 02:21:54] Reporting output tracks
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[2018-10-13 02:25:04] A summary of the alignment counts can be found in /scratch/8792902.1.linga/tophat2/align_summary.txt
[2018-10-13 02:25:04] Run complete: 00:25:35 elapsed