[2018-10-12 22:18:58] Beginning TopHat run (v2.1.1)
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[2018-10-12 22:18:58] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 22:18:58] Checking for Bowtie index files (genome)..
[2018-10-12 22:18:58] Checking for reference FASTA file
[2018-10-12 22:18:58] Generating SAM header for Bowtie2Index/genome
[2018-10-12 22:19:02] Reading known junctions from GTF file
[2018-10-12 22:19:06] Preparing reads
	 left reads: min. length=100, max. length=100, 298153 kept reads (201 discarded)
	right reads: min. length=100, max. length=100, 297938 kept reads (416 discarded)
[2018-10-12 22:19:20] Building transcriptome data files /scratch/8792790.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 22:19:40] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 22:27:55] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:28:28] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 22:29:00] Resuming TopHat pipeline with unmapped reads
[2018-10-12 22:29:00] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:29:35] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:29:43] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:29:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:30:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:30:13] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 22:30:49] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 22:30:59] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 22:31:11] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 22:31:21] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 22:31:30] Searching for junctions via segment mapping
[2018-10-12 22:34:02] Retrieving sequences for splices
[2018-10-12 22:36:13] Indexing splices
[2018-10-12 22:36:33] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:36:37] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:36:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:36:46] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:36:50] Joining segment hits
[2018-10-12 22:39:05] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 22:39:09] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 22:39:14] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 22:39:18] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 22:39:22] Joining segment hits
[2018-10-12 22:41:39] Reporting output tracks
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[2018-10-12 22:44:46] A summary of the alignment counts can be found in /scratch/8792790.1.linga/tophat2/align_summary.txt
[2018-10-12 22:44:46] Run complete: 00:25:48 elapsed