[2019-04-29 17:27:33] Beginning TopHat run (v2.1.1)
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[2019-04-29 17:27:33] Checking for Bowtie
		  Bowtie version:	 2.2.4.0
[2019-04-29 17:27:34] Checking for Bowtie index files (genome)..
[2019-04-29 17:27:34] Checking for reference FASTA file
[2019-04-29 17:27:34] Generating SAM header for Bowtie2Index/genome
[2019-04-29 17:27:36] Reading known junctions from GTF file
[2019-04-29 17:27:38] Preparing reads
	 left reads: min. length=50, max. length=50, 72135222 kept reads (20476 discarded)
	right reads: min. length=50, max. length=50, 72109226 kept reads (46472 discarded)
[2019-04-29 17:50:02] Building transcriptome data files /scratch/5765364.1.p/tophat2/tmp/RefSeq_GeneBody
[2019-04-29 17:50:12] Building Bowtie index from RefSeq_GeneBody.fa
[2019-04-29 17:55:06] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 18:11:27] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-04-29 18:27:14] Resuming TopHat pipeline with unmapped reads
[2019-04-29 18:27:15] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 18:41:55] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 18:44:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 18:46:40] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-04-29 19:02:00] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/2)
[2019-04-29 19:06:08] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/2)
[2019-04-29 19:29:23] Searching for junctions via segment mapping
[2019-04-29 19:34:52] Retrieving sequences for splices
[2019-04-29 19:35:52] Indexing splices
[2019-04-29 19:36:05] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 19:36:49] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 19:37:39] Joining segment hits
[2019-04-29 19:39:02] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/2)
[2019-04-29 19:40:02] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/2)
[2019-04-29 19:41:20] Joining segment hits
[2019-04-29 19:43:23] Reporting output tracks
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[2019-04-29 20:36:35] A summary of the alignment counts can be found in /scratch/5765364.1.p/tophat2/align_summary.txt
[2019-04-29 20:36:35] Run complete: 03:09:01 elapsed