[2024-04-23 12:32:19] Beginning TopHat run (v2.0.14) ----------------------------------------------- [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, 46964897 kept reads (451 discarded) [2024-04-23 12:39:34] Building transcriptome data files /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K7_08596/tmp/refGene [2024-04-23 12:39:46] Building Bowtie index from refGene.fa [2024-04-23 12:49:52] Mapping left_kept_reads to transcriptome refGene with Bowtie [2024-04-23 13:17:55] Resuming TopHat pipeline with unmapped reads [2024-04-23 13:17:55] Mapping left_kept_reads.m2g_um to genome genome with Bowtie [2024-04-23 13:22:02] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie (1/2) [2024-04-23 13:26:24] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie (2/2) [2024-04-23 13:30:31] Searching for junctions via segment mapping [2024-04-23 13:32:44] Retrieving sequences for splices [2024-04-23 13:34:11] Indexing splices [2024-04-23 13:34:24] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie (1/2) [2024-04-23 13:35:00] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie (2/2) [2024-04-23 13:35:34] Joining segment hits [2024-04-23 13:37:10] Reporting output tracks ----------------------------------------------- [2024-04-23 13:49:52] A summary of the alignment counts can be found in /no_backup/ldicroce/eblanco/molbio/02_map_files/mm10/RNA_114K7_08596/align_summary.txt [2024-04-23 13:49:52] Run complete: 01:17:33 elapsed