Question: GLIMMER: failed to create PWM?
0
gravatar for niuzx9581
17 months ago by
niuzx958110
niuzx958110 wrote:

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
glimmer • 523 views
ADD COMMENTlink modified 17 months ago by ATpoint40k • written 17 months ago by niuzx958110
1

do these awk command exist?

ls /root/biotools/glimmer3.02/scripts/upstream-coords.awk
ls /root/biotools/glimmer3.02/scripts/get-motif-counts.aw

did you install elph?

Note that some tools called by g3-iterated.csh don't work on multi fasta files. You may want to look into the more recent prodigal

ADD REPLYlink written 17 months ago by Carambakaracho2.2k
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