[2019-04-29 17:42:40] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:42:40] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:42:43] Checking for Bowtie index files (genome)..
[2019-04-29 17:42:43] Checking for reference FASTA file
[2019-04-29 17:42:43] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:44:23] Reading known junctions from GTF file
[2019-04-29 17:44:27] Preparing reads
	 left reads: min. length=50, max. length=50, 92536228 kept reads (37867 discarded)
	right reads: min. length=50, max. length=50, 92487148 kept reads (86947 discarded)
[2019-04-29 18:38:39] Building transcriptome data files /scratch/5765373.1.linga/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 18:39:00] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 18:50:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 20:26:55] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 21:46:54] Resuming TopHat pipeline with unmapped reads
[2019-04-29 21:46:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 22:05:08] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 22:08:31] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 22:10:09] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 22:24:27] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 22:26:56] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 22:29:26] Searching for junctions via segment mapping
[2019-04-29 22:36:39] Retrieving sequences for splices
[2019-04-29 22:38:45] Indexing splices
[2019-04-29 22:39:11] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 22:39:46] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 22:40:17] Joining segment hits
[2019-04-29 22:43:18] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 22:43:53] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 22:44:27] Joining segment hits
[2019-04-29 22:47:17] Reporting output tracks
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[2019-04-30 00:57:43] A summary of the alignment counts can be found in /scratch/5765373.1.linga/tophat2/align_summary.txt
[2019-04-30 00:57:43] Run complete: 07:15:03 elapsed