[2024-04-23 12:32:19] Beginning TopHat run (v2.0.14)
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[2024-04-23 12:32:19] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
		  Bowtie version:	 1.1.1.0
[2024-04-23 12:32:19] Checking for Bowtie index files (genome)..
[2024-04-23 12:32:19] Checking for reference FASTA file
[2024-04-23 12:32:19] Generating SAM header for /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome
[2024-04-23 12:32:21] Reading known junctions from GTF file
[2024-04-23 12:32:25] Preparing reads
	 left reads: min. length=50, max. length=50, 46323580 kept reads (278 discarded)
[2024-04-23 12:39:31] Building transcriptome data files /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114P_08592/tmp/refGene
[2024-04-23 12:39:44] Building Bowtie index from refGene.fa
[2024-04-23 12:49:49] Mapping left_kept_reads to transcriptome refGene with Bowtie 
[2024-04-23 13:17:23] Resuming TopHat pipeline with unmapped reads
[2024-04-23 13:17:23] Mapping left_kept_reads.m2g_um to genome genome with Bowtie 
[2024-04-23 13:21:29] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie (1/2)
[2024-04-23 13:25:25] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie (2/2)
[2024-04-23 13:29:16] Searching for junctions via segment mapping
[2024-04-23 13:31:28] Retrieving sequences for splices
[2024-04-23 13:32:55] Indexing splices
[2024-04-23 13:33:08] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/2)
[2024-04-23 13:33:42] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie (2/2)
[2024-04-23 13:34:16] Joining segment hits
[2024-04-23 13:35:51] Reporting output tracks
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[2024-04-23 13:48:34] A summary of the alignment counts can be found in /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114P_08592/align_summary.txt
[2024-04-23 13:48:34] Run complete: 01:16:15 elapsed