[2019-06-26 17:47:15] Beginning TopHat run (v2.1.1)
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[2019-06-26 17:47:15] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2019-06-26 17:47:16] Checking for Bowtie index files (genome)..
[2019-06-26 17:47:16] Checking for reference FASTA file
[2019-06-26 17:47:16] Generating SAM header for Bowtie2Index/genome
[2019-06-26 17:47:21] Reading known junctions from GTF file
[2019-06-26 17:47:25] Preparing reads
	 left reads: min. length=35, max. length=76, 25712251 kept reads (1051328 discarded)
	right reads: min. length=35, max. length=76, 26506981 kept reads (256598 discarded)
[2019-06-26 18:07:49] Building transcriptome data files /scratch/7076179.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-06-26 18:08:12] Building Bowtie index from RefSeq_GeneBody.fa
[2019-06-26 18:16:04] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 18:35:25] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-06-26 19:03:52] Resuming TopHat pipeline with unmapped reads
[2019-06-26 19:03:53] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 19:16:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 19:19:04] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 19:22:14] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 19:25:31] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-06-26 19:43:41] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2019-06-26 19:49:18] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2019-06-26 19:54:46] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2019-06-26 20:00:45] Searching for junctions via segment mapping
[2019-06-26 20:10:55] Retrieving sequences for splices
[2019-06-26 20:13:19] Indexing splices
[2019-06-26 20:13:40] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 20:13:51] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 20:14:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 20:16:04] Joining segment hits
[2019-06-26 20:20:29] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2019-06-26 20:20:46] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2019-06-26 20:22:33] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2019-06-26 20:25:23] Joining segment hits
[2019-06-26 20:30:13] Reporting output tracks
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[2019-06-27 00:17:10] A summary of the alignment counts can be found in /scratch/7076179.1.linga/tophat2/align_summary.txt
[2019-06-27 00:17:10] Run complete: 06:29:54 elapsed