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File path #1
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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 |
Hi Jeff, Did this solution work? Kind regards, |
Hi Matt, thanks for the suggestion. Haven't had a chance today sorry. Will let you know asap
Many Thanks,Jeff
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Subject: Re: [MatthewHiggins2017/bioconda-PrimedRPA] File path (#1)
Hi Jeff,
Did this solution work?
Kind regards,
Matt.
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Hi Matt, yeah, that seems to have worked thanks: 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 Any suggestions? |
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? Generating Alignment Summary (fine!) The above exception was the direct cause of the following exception: Traceback (most recent call last): -- |
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 |
Many thanks Matt. Did that via Let me know if you'd like me to run anything and let you know the error output Jeff |
Hi Matt, Have you had a chance to take a look at this please? Cheers, Jeff |
Had a similar problem installed samtools and updated it and the program works |
Hi,
Stumbling on the walk through here: after copying new parameters to file program doesn't recognise the file path for Step 3.
Have re-started terminal, restarted machine and checked all file paths within the Parameters file.
Any ideas please?
(base) jeff@UBU-CND7483XVZ:
$ cd ./Walk_Through_RPA_Primers//Walk_Through_RPA_Primers$ ls -l(base) jeff@UBU-CND7483XVZ:
total 1704
-rw-r--r-- 1 jeff jeff 7478 May 15 2015 GCF_000896435.1_ViralProj76727_genomic.fna
-rw-r--r-- 1 jeff jeff 94163 May 19 12:06 HPV_Run_1_Alignment_Summary.csv
-rw-r--r-- 1 jeff jeff 237945 May 19 12:06 HPV_Run_1_Output_Sets.csv
-rw-r--r-- 1 jeff jeff 1393632 May 19 12:06 HPV_Run_1_PrimedRPA_Oligo_Binding_Sites.csv
-rw-r--r-- 1 jeff jeff 2378 May 19 12:16 PrimedRPA_Parameters.txt
(base) jeff@UBU-CND7483XVZ:~/Walk_Through_RPA_Primers$ PrimedRPA PrimedRPA_Parameters.txt
----------------PrimedRPA------------------
-----Finding RPA Primer and Probe Sets-----
-------------Higgins M et al.--------------
Parameters File Could Not Be Opened
Check File Path.
PLease run PrimedRPA --help to see valid options
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