Hi everyone, I encountered a very strange problems when I use the g3-iterated.csh of GLIMMER to identify protein-coding genes in Wolbachia spp.
I tried to reinstall the software, but it still didn't work, and I have root, I don't know why there is such a problem. I also modified the installation path in script.
root@huawei:~/biotools/glimmer3.02/scripts# csh ./g3-iterated.csh ~/biotools/Spicta_Wolbachia.fa wpic Step 1 of 8: Finding long orfs for training Starting at Thu May 23 22:21:36 2019 Sequence file = /root/biotools/Spicta_Wolbachia.fa Excluded regions file = none Circular genome = true Initial minimum gene length = 90 bp Determine optimal min gene length to maximize number of genes Maximum overlap bases = 30 Start codons = atg,gtg,ttg Stop codons = taa,tag,tga Sequence length = 1380688 Final minimum gene length = 343 Number of genes = 891 Total bases = 896733 Step 2 of 8: Extracting training sequences Step 3 of 8: Building ICM Step 4 of 8: Running first Glimmer3 Starting at Thu May 23 22:21:40 2019 Sequence file = /root/biotools/Spicta_Wolbachia.fa Number of sequences = 3 ICM model file = wpic.icm Excluded regions file = none List of orfs file = none Input is NOT separate orfs Independent (non-coding) scores are used Circular genome = true Truncated orfs = false Minimum gene length = 110 bp Maximum overlap bases = 50 Threshold score = 30 Use first start codon = false Start codons = atg,gtg,ttg Start probs = 0.600,0.300,0.100 Stop codons = taa,tag,tga GC percentage = 33.9% Ignore score on orfs longer than 487 Analyzing Sequence #1 Start Find_Orfs Start Score_Orfs Start Process_Events Start Trace_Back Analyzing Sequence #2 Start Find_Orfs Start Score_Orfs Start Process_Events Start Trace_Back Analyzing Sequence #3 Start Find_Orfs Start Score_Orfs Start Process_Events Start Trace_Back Step 5 of 8: Getting training coordinates Step 6 of 8: Making PWM from upstream regions /root/biotools/glimmer3.02/scripts/upstream-coords.awk: Command not found. /root/biotools/ELPH/bin/: Permission denied. /root/biotools/glimmer3.02/scripts/get-motif-counts.awk: Command not found. Failed to create PWM