[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 12:32:06] Reading known junctions from GTF file
[2024-04-23 12:32:10] Preparing reads
	 left reads: min. length=50, max. length=50, 47398751 kept reads (445 discarded)
[2024-04-23 12:38:26] Building transcriptome data files /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW1_08587/tmp/refGene
[2024-04-23 12:38:39] Building Bowtie index from refGene.fa
[2024-04-23 12:50:29] Mapping left_kept_reads to transcriptome refGene with Bowtie 
[2024-04-23 13:20:21] Resuming TopHat pipeline with unmapped reads
[2024-04-23 13:20:21] Mapping left_kept_reads.m2g_um to genome genome with Bowtie 
[2024-04-23 13:24:44] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie (1/2)
[2024-04-23 13:29:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie (2/2)
[2024-04-23 13:33:57] Searching for junctions via segment mapping
[2024-04-23 13:36:17] Retrieving sequences for splices
[2024-04-23 13:37:47] Indexing splices
[2024-04-23 13:38:02] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/2)
[2024-04-23 13:38:44] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie (2/2)
[2024-04-23 13:39:26] Joining segment hits
[2024-04-23 13:41:08] Reporting output tracks
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[2024-04-23 13:54:36] A summary of the alignment counts can be found in /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_PrEW1_08587/align_summary.txt
[2024-04-23 13:54:36] Run complete: 01:22:33 elapsed