[2019-06-26 16:00:55] Beginning TopHat run (v2.1.1)
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[2019-06-26 16:00:55] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 16:00:55] Checking for Bowtie index files (genome)..
[2019-06-26 16:00:55] Checking for reference FASTA file
[2019-06-26 16:00:55] Generating SAM header for Bowtie2Index/genome
[2019-06-26 16:00:59] Reading known junctions from GTF file
[2019-06-26 16:01:02] Preparing reads
	 left reads: min. length=35, max. length=76, 23148647 kept reads (702574 discarded)
	right reads: min. length=35, max. length=76, 23664951 kept reads (186270 discarded)
[2019-06-26 16:15:44] Building transcriptome data files /scratch/7076174.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 16:16:00] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 16:22:16] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 16:35:47] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 16:49:43] Resuming TopHat pipeline with unmapped reads
[2019-06-26 16:49:43] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 16:57:58] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 17:00:07] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 17:02:22] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 17:04:37] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 17:14:43] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 17:18:37] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 17:21:55] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 17:25:18] Searching for junctions via segment mapping
[2019-06-26 17:32:51] Retrieving sequences for splices
[2019-06-26 17:35:22] Indexing splices
[2019-06-26 17:35:41] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 17:35:50] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 17:36:47] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 17:37:53] Joining segment hits
[2019-06-26 17:41:39] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 17:41:55] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 17:42:56] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 17:44:35] Joining segment hits
[2019-06-26 17:48:49] Reporting output tracks
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[2019-06-26 20:06:42] A summary of the alignment counts can be found in /scratch/7076174.1.linga/tophat2/align_summary.txt
[2019-06-26 20:06:42] Run complete: 04:05:46 elapsed