[2024-04-23 12:32:18] Beginning TopHat run (v2.0.14)
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[2024-04-23 12:32:18] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
		  Bowtie version:	 1.1.1.0
[2024-04-23 12:32:18] Checking for Bowtie index files (genome)..
[2024-04-23 12:32:18] Checking for reference FASTA file
[2024-04-23 12:32:18] Generating SAM header for /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome
[2024-04-23 12:32:20] Reading known junctions from GTF file
[2024-04-23 12:32:24] Preparing reads
	 left reads: min. length=50, max. length=50, 45478961 kept reads (566 discarded)
[2024-04-23 12:38:34] Building transcriptome data files /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K8_08597/tmp/refGene
[2024-04-23 12:38:48] Building Bowtie index from refGene.fa
[2024-04-23 12:50:18] Mapping left_kept_reads to transcriptome refGene with Bowtie 
[2024-04-23 13:22:23] Resuming TopHat pipeline with unmapped reads
[2024-04-23 13:22:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie 
[2024-04-23 13:25:48] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie (1/2)
[2024-04-23 13:30:10] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie (2/2)
[2024-04-23 13:34:22] Searching for junctions via segment mapping
[2024-04-23 13:36:42] Retrieving sequences for splices
[2024-04-23 13:38:13] Indexing splices
[2024-04-23 13:38:27] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/2)
[2024-04-23 13:39:04] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie (2/2)
[2024-04-23 13:39:41] Joining segment hits
[2024-04-23 13:41:22] Reporting output tracks
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[2024-04-23 13:54:38] A summary of the alignment counts can be found in /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K8_08597/align_summary.txt
[2024-04-23 13:54:38] Run complete: 01:22:20 elapsed