[2024-04-23 12:32:17] Beginning TopHat run (v2.0.14)
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[2024-04-23 12:32:17] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
		  Bowtie version:	 1.1.1.0
[2024-04-23 12:32:17] Checking for Bowtie index files (genome)..
[2024-04-23 12:32:17] Checking for reference FASTA file
[2024-04-23 12:32:17] Generating SAM header for /no_backup/ldicroce/eblanco/molbio/indexes/mm10/genome
[2024-04-23 12:32:19] Reading known junctions from GTF file
[2024-04-23 12:32:23] Preparing reads
	 left reads: min. length=50, max. length=50, 46319406 kept reads (215 discarded)
[2024-04-23 12:39:26] Building transcriptome data files /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W3_08594/tmp/refGene
[2024-04-23 12:39:38] Building Bowtie index from refGene.fa
[2024-04-23 12:50:34] Mapping left_kept_reads to transcriptome refGene with Bowtie 
[2024-04-23 13:25:52] Resuming TopHat pipeline with unmapped reads
[2024-04-23 13:25:52] Mapping left_kept_reads.m2g_um to genome genome with Bowtie 
[2024-04-23 13:29:47] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie (1/2)
[2024-04-23 13:33:53] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie (2/2)
[2024-04-23 13:37:53] Searching for junctions via segment mapping
[2024-04-23 13:40:05] Retrieving sequences for splices
[2024-04-23 13:41:31] Indexing splices
[2024-04-23 13:41:44] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/2)
[2024-04-23 13:42:16] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie (2/2)
[2024-04-23 13:42:49] Joining segment hits
[2024-04-23 13:44:23] Reporting output tracks
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[2024-04-23 13:57:06] A summary of the alignment counts can be found in /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114W3_08594/align_summary.txt
[2024-04-23 13:57:06] Run complete: 01:24:48 elapsed