Comments (9)
Hi Jeff,
First could you please double check the PrimedRPA_Parameters.txt file contains all 22, greater than symbols '>' as if there are more or less, this could trigger the error. This could be done with the following command: grep '>' PrimedRPA_Parameters.txt | wc -l
Alternatively, if this doesnt work, could you please try the command-line option by running the following command:
PrimedRPA --RunID Debug --InputFile GCF_000896435.1_ViralProj76727_genomic.fna
from bioconda-primedrpa.
Hi Jeff,
Did this solution work?
Kind regards,
Matt.
from bioconda-primedrpa.
from bioconda-primedrpa.
Hi Matt, yeah, that seems to have worked thanks:
22 '>'s and your files produced three debug_...csv files, with less oligo binding sites than the first.
Now for step 3 and it's produced a folder with blast inputs and outputs, but come up with an error message saying it can't find the
ileNotFoundError: [Errno 2] No such file or directory: 'Adv_TAAGACCGCCTTCGGTCTATAAATTCACAGAG_AF082339.1.fa'
Any suggestions?
Many Thanks, Jeff
from bioconda-primedrpa.
Hi Matt,
Got round to having a go with my own data today. Fine when I'm just producing primers, probes and self-annealing scores, but getting an error when I attempat a cross-reactivity file. Have checked file paths, formatting trimmed sequences to equal length. Seems to be an error with the Blast search of the non-target sequences. Any suggestions please?
Error message when running from scratch i.e. without providing a previously generated alignment File/Binding sites:
Generating Alignment Summary (fine!)
Generating Primer/Probe Binding Site DataFrame
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/jeff/miniconda3/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/jeff/miniconda3/lib/python3.7/multiprocessing/pool.py", line 47, in starmapstar
return list(itertools.starmap(args[0], args[1]))
File "/home/jeff/miniconda3/bin/PrimedRPA", line 541, in IndentifyingAndFilteringOligos
MaxBackgroundScoreBindingScore, MaxScoreBackSeq, HardFailBool = BlastnBackgroundCheck(NucleotideSeq, AllParameter)
File "/home/jeff/miniconda3/bin/PrimedRPA", line 195, in BlastnBackgroundCheck
fastadict = FastaToDict('Adv_{}_{}.fa'.format(seq,CleanRefID))
File "/home/jeff/miniconda3/bin/PrimedRPA", line 32, in FastaToDict
with open(InputFile) as file_one:
FileNotFoundError: [Errno 2] No such file or directory: 'Adv_GTTGAATATTTACTTTAGATCATAAGCGGGTTGG_AB597287.1.fa'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/jeff/miniconda3/bin/PrimedRPA", line 1034, in
CheckingAlignedOutputFile(AllParameter)
File "/home/jeff/miniconda3/bin/PrimedRPA", line 810, in CheckingAlignedOutputFile
PotentialPrimerProbeOut = pool.starmap(IndentifyingAndFilteringOligos,PrimerProbeCheckParallelInput)
File "/home/jeff/miniconda3/lib/python3.7/multiprocessing/pool.py", line 276, in starmap
return self._map_async(func, iterable, starmapstar, chunksize).get()
File "/home/jeff/miniconda3/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: 'Adv_GTTGAATATTTACTTTAGATCATAAGCGGGTTGG_AB597287.1.fa'
--
Much appreciated, Jeff
from bioconda-primedrpa.
Hi Jeff,
Apologies for the delay in my response and can you please check the version of samtools have installed with bioconda is v1.9 or higher
from bioconda-primedrpa.
Many thanks Matt. Did that via
conda update samtools
and it's upgraded from v1.3.1 to 1.9, but still the same error message.
Let me know if you'd like me to run anything and let you know the error output
Jeff
from bioconda-primedrpa.
Hi Matt,
Have you had a chance to take a look at this please?
Cheers, Jeff
from bioconda-primedrpa.
Had a similar problem installed samtools and updated it and the program works
from bioconda-primedrpa.
Related Issues (11)
- Need guide to Primed RPA HOT 5
- Parameters File Could Not Be Opened
- PrimeRPA failing with "return object.__getattribute__(self, name) AttributeError: 'DataFrame' object has no attribute 'append'" error
- FileNotFoundError: [Errno 2] No such file or directory: HOT 7
- Index Error: list index out of range HOT 3
- Old Primed RPA files HOT 1
- Error in running PrimedRPA HOT 4
- PrimedRPA_Walkthrough_Challenge HOT 1
- UnboundLocalError HOT 4
- KeyError: 'Advanced Cross Reactivity Percentage'
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bioconda-primedrpa.