[2020-03-09 07:50:49] Beginning TopHat run (v2.1.1)
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[2020-03-09 07:50:49] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 07:50:49] Checking for Bowtie index files (genome)..
[2020-03-09 07:50:49] Checking for reference FASTA file
[2020-03-09 07:50:49] Generating SAM header for Bowtie2Index/genome
[2020-03-09 07:50:50] Reading known junctions from GTF file
[2020-03-09 07:50:53] Preparing reads
	 left reads: min. length=75, max. length=75, 24661281 kept reads (11265 discarded)
[2020-03-09 07:55:44] Building transcriptome data files /scratch/3763325.1.c/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 07:55:53] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 08:00:20] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 08:06:26] Resuming TopHat pipeline with unmapped reads
[2020-03-09 08:06:26] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 08:13:16] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 08:14:02] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 08:14:46] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 08:15:24] Searching for junctions via segment mapping
[2020-03-09 08:17:03] Retrieving sequences for splices
[2020-03-09 08:18:08] Indexing splices
[2020-03-09 08:18:19] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 08:18:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 08:18:42] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 08:18:51] Joining segment hits
[2020-03-09 08:20:17] Reporting output tracks
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[2020-03-09 08:35:42] A summary of the alignment counts can be found in /scratch/3763325.1.c/tophat2/align_summary.txt
[2020-03-09 08:35:42] Run complete: 00:44:53 elapsed