[2018-10-13 12:24:28] Beginning TopHat run (v2.1.1)
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[2018-10-13 12:24:28] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 12:24:28] Checking for Bowtie index files (genome)..
[2018-10-13 12:24:28] Checking for reference FASTA file
[2018-10-13 12:24:28] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:24:33] Reading known junctions from GTF file
[2018-10-13 12:24:38] Preparing reads
	 left reads: min. length=100, max. length=100, 1105243 kept reads (230 discarded)
	right reads: min. length=100, max. length=100, 1105034 kept reads (439 discarded)
[2018-10-13 12:25:23] Building transcriptome data files /scratch/8793232.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:25:42] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:34:05] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:39:22] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:44:21] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:44:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:45:21] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:45:41] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:46:21] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:46:48] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:47:10] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:48:09] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:48:29] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:49:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:49:40] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:50:07] Searching for junctions via segment mapping
[2018-10-13 13:11:10] Retrieving sequences for splices
[2018-10-13 13:13:21] Indexing splices
[2018-10-13 13:13:53] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:14:25] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:15:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:15:40] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:16:04] Joining segment hits
[2018-10-13 13:18:42] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:19:08] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:19:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:20:26] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:20:55] Joining segment hits
[2018-10-13 13:24:10] Reporting output tracks
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[2018-10-13 14:30:46] A summary of the alignment counts can be found in /scratch/8793232.1.linga/tophat2/align_summary.txt
[2018-10-13 14:30:46] Run complete: 02:06:17 elapsed