[2019-05-08 08:48:03] Beginning TopHat run (v2.1.1)
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[2019-05-08 08:48:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2019-05-08 08:48:03] Checking for Bowtie index files (genome)..
[2019-05-08 08:48:03] Checking for reference FASTA file
[2019-05-08 08:48:03] Generating SAM header for Bowtie2Index/genome
[2019-05-08 08:48:05] Reading known junctions from GTF file
[2019-05-08 08:48:07] Preparing reads
	 left reads: min. length=101, max. length=101, 38533580 kept reads (342457 discarded)
[2019-05-08 08:58:28] Building transcriptome data files /scratch/5992725.1.p8/tophat2/tmp/RefSeq_GeneBody
[2019-05-08 08:58:37] Building Bowtie index from RefSeq_GeneBody.fa
[2019-05-08 09:03:32] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2019-05-08 09:16:55] Resuming TopHat pipeline with unmapped reads
[2019-05-08 09:16:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2019-05-08 09:23:52] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2019-05-08 09:24:32] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2019-05-08 09:25:18] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2019-05-08 09:26:04] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2019-05-08 09:26:55] Searching for junctions via segment mapping
[2019-05-08 09:33:37] Retrieving sequences for splices
[2019-05-08 09:34:44] Indexing splices
[2019-05-08 09:35:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2019-05-08 09:35:36] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2019-05-08 09:35:52] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2019-05-08 09:36:09] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2019-05-08 09:36:27] Joining segment hits
[2019-05-08 09:38:08] Reporting output tracks
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[2019-05-08 09:49:12] A summary of the alignment counts can be found in /scratch/5992725.1.p8/tophat2/align_summary.txt
[2019-05-08 09:49:12] Run complete: 01:01:09 elapsed