[2020-03-09 05:49:10] Beginning TopHat run (v2.1.1)
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[2020-03-09 05:49:10] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 05:49:11] Checking for Bowtie index files (genome)..
[2020-03-09 05:49:11] Checking for reference FASTA file
[2020-03-09 05:49:11] Generating SAM header for Bowtie2Index/genome
[2020-03-09 05:49:18] Reading known junctions from GTF file
[2020-03-09 05:49:22] Preparing reads
	 left reads: min. length=75, max. length=75, 30315875 kept reads (17126 discarded)
[2020-03-09 06:00:40] Building transcriptome data files /scratch/3763306.1.linga/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 06:01:01] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 06:09:08] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 06:22:39] Resuming TopHat pipeline with unmapped reads
[2020-03-09 06:22:40] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 06:45:23] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 06:47:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 06:50:03] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 06:52:17] Searching for junctions via segment mapping
[2020-03-09 06:57:04] Retrieving sequences for splices
[2020-03-09 06:59:36] Indexing splices
[2020-03-09 07:00:00] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 07:00:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 07:01:06] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 07:01:33] Joining segment hits
[2020-03-09 07:05:15] Reporting output tracks
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[2020-03-09 07:35:02] A summary of the alignment counts can be found in /scratch/3763306.1.linga/tophat2/align_summary.txt
[2020-03-09 07:35:02] Run complete: 01:45:51 elapsed