[2024-04-23 12:32:03] Beginning TopHat run (v2.0.14)
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[2024-04-23 12:32:03] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
		  Bowtie version:	 1.1.1.0
[2024-04-23 12:32:03] Checking for Bowtie index files (genome)..
[2024-04-23 12:32:03] Checking for reference FASTA file
[2024-04-23 12:32:03] Generating SAM header for /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome
[2024-04-23 12:32:07] Reading known junctions from GTF file
[2024-04-23 12:32:11] Preparing reads
	 left reads: min. length=50, max. length=50, 46035534 kept reads (438 discarded)
[2024-04-23 12:39:12] Building transcriptome data files /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW3_08588/tmp/refGene
[2024-04-23 12:39:25] Building Bowtie index from refGene.fa
[2024-04-23 12:50:12] Mapping left_kept_reads to transcriptome refGene with Bowtie 
[2024-04-23 13:25:07] Resuming TopHat pipeline with unmapped reads
[2024-04-23 13:25:07] Mapping left_kept_reads.m2g_um to genome genome with Bowtie 
[2024-04-23 13:29:10] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie (1/2)
[2024-04-23 13:33:54] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie (2/2)
[2024-04-23 13:38:27] Searching for junctions via segment mapping
[2024-04-23 13:40:41] Retrieving sequences for splices
[2024-04-23 13:42:05] Indexing splices
[2024-04-23 13:42:20] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/2)
[2024-04-23 13:42:57] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie (2/2)
[2024-04-23 13:43:33] Joining segment hits
[2024-04-23 13:45:11] Reporting output tracks
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[2024-04-23 13:57:43] A summary of the alignment counts can be found in /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW3_08588/align_summary.txt
[2024-04-23 13:57:43] Run complete: 01:25:39 elapsed