[2018-10-12 23:31:55] Beginning TopHat run (v2.1.1)
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[2018-10-12 23:31:55] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-12 23:31:55] Checking for Bowtie index files (genome)..
[2018-10-12 23:31:55] Checking for reference FASTA file
[2018-10-12 23:31:55] Generating SAM header for Bowtie2Index/genome
[2018-10-12 23:31:59] Reading known junctions from GTF file
[2018-10-12 23:32:04] Preparing reads
	 left reads: min. length=100, max. length=100, 168170 kept reads (282 discarded)
	right reads: min. length=100, max. length=100, 168011 kept reads (441 discarded)
[2018-10-12 23:32:11] Building transcriptome data files /scratch/8792839.1.linga/tophat2/tmp/RefSeq_GeneBody
[2018-10-12 23:32:31] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-12 23:40:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:41:16] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-12 23:42:02] Resuming TopHat pipeline with unmapped reads
[2018-10-12 23:42:19] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:42:51] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:43:49] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:44:16] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:44:26] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:44:36] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-12 23:45:06] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-12 23:45:16] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-12 23:45:29] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-12 23:45:38] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-12 23:45:48] Searching for junctions via segment mapping
[2018-10-12 23:48:18] Retrieving sequences for splices
[2018-10-12 23:50:28] Indexing splices
[2018-10-12 23:50:50] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:50:54] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:50:59] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:51:03] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:51:07] Joining segment hits
[2018-10-12 23:53:34] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-12 23:53:39] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-12 23:53:44] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-12 23:53:48] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-12 23:53:52] Joining segment hits
[2018-10-12 23:56:09] Reporting output tracks
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[2018-10-12 23:58:54] A summary of the alignment counts can be found in /scratch/8792839.1.linga/tophat2/align_summary.txt
[2018-10-12 23:58:54] Run complete: 00:26:58 elapsed