[2020-03-09 05:47:03] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:47:03] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:47:09] Checking for Bowtie index files (genome)..
[2020-03-09 05:47:09] Checking for reference FASTA file
[2020-03-09 05:47:09] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:47:13] Reading known junctions from GTF file
[2020-03-09 05:47:21] Preparing reads
	 left reads: min. length=75, max. length=75, 37422186 kept reads (22071 discarded)
[2020-03-09 06:00:18] Building transcriptome data files /scratch/3763308.1.linga/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 06:00:37] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 06:07:48] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:21:21] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:21:22] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:48:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:51:23] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:54:12] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:57:04] Searching for junctions via segment mapping
[2020-03-09 07:01:02] Retrieving sequences for splices
[2020-03-09 07:03:14] Indexing splices
[2020-03-09 07:03:42] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 07:04:24] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 07:05:05] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 07:05:40] Joining segment hits
[2020-03-09 07:08:53] Reporting output tracks
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[2020-03-09 07:37:43] A summary of the alignment counts can be found in /scratch/3763308.1.linga/tophat2/align_summary.txt
[2020-03-09 07:37:43] Run complete: 01:50:39 elapsed