[2018-10-13 11:59:57] Beginning TopHat run (v2.1.1)
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[2018-10-13 11:59:57] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 11:59:58] Checking for Bowtie index files (genome)..
[2018-10-13 11:59:58] Checking for reference FASTA file
[2018-10-13 11:59:58] Generating SAM header for Bowtie2Index/genome
[2018-10-13 12:00:02] Reading known junctions from GTF file
[2018-10-13 12:00:07] Preparing reads
	 left reads: min. length=100, max. length=100, 2592078 kept reads (824 discarded)
	right reads: min. length=100, max. length=100, 2591545 kept reads (1357 discarded)
[2018-10-13 12:01:48] Building transcriptome data files /scratch/8793224.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 12:02:10] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 12:10:54] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:18:29] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 12:26:18] Resuming TopHat pipeline with unmapped reads
[2018-10-13 12:26:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:27:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:28:22] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:29:19] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:29:57] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:30:45] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 12:32:21] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 12:32:44] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 12:33:41] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 12:34:22] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 12:35:09] Searching for junctions via segment mapping
[2018-10-13 13:01:48] Retrieving sequences for splices
[2018-10-13 13:04:01] Indexing splices
[2018-10-13 13:04:29] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:04:56] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:05:51] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:06:41] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:07:34] Joining segment hits
[2018-10-13 13:10:33] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 13:11:01] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 13:11:59] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 13:12:52] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 13:13:44] Joining segment hits
[2018-10-13 13:16:43] Reporting output tracks
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[2018-10-13 15:02:59] A summary of the alignment counts can be found in /scratch/8793224.1.linga/tophat2/align_summary.txt
[2018-10-13 15:02:59] Run complete: 03:03:01 elapsed