[2020-03-09 07:02:13] Beginning TopHat run (v2.1.1)
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[2020-03-09 07:02:13] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 07:02:13] Checking for Bowtie index files (genome)..
[2020-03-09 07:02:13] Checking for reference FASTA file
[2020-03-09 07:02:13] Generating SAM header for Bowtie2Index/genome
[2020-03-09 07:02:14] Reading known junctions from GTF file
[2020-03-09 07:02:16] Preparing reads
	 left reads: min. length=75, max. length=75, 24417351 kept reads (12845 discarded)
[2020-03-09 07:07:05] Building transcriptome data files /scratch/3763322.1.c/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 07:07:14] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 07:11:47] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 07:19:03] Resuming TopHat pipeline with unmapped reads
[2020-03-09 07:19:03] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 07:26:19] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 07:27:08] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 07:27:55] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 07:28:35] Searching for junctions via segment mapping
[2020-03-09 07:30:59] Retrieving sequences for splices
[2020-03-09 07:32:04] Indexing splices
[2020-03-09 07:32:18] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 07:32:35] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 07:32:50] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 07:33:02] Joining segment hits
[2020-03-09 07:34:31] Reporting output tracks
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[2020-03-09 07:50:40] A summary of the alignment counts can be found in /scratch/3763322.1.c/tophat2/align_summary.txt
[2020-03-09 07:50:40] Run complete: 00:48:27 elapsed