Closed silenus092 closed 3 years ago
Hello,
To solve this use the PATH
instead of .
Example:
bash precheck_TransPi.sh /home/ubuntu/TransPi
I'll try to find a way how to solve this for future updates.
Thanks
Thank you I now made it runnable, btw I have a small question
How to select Kmers number?
I saw the list of number in GitHub doc. or in your paper for example ;
--k 25,41,53 --maxReadLen 75
However, still, I do not fully understand how to related these (e.g., 25,41,53 )number to the sequence length
If I have
file format type num_seqs sum_len min_len avg_len max_len
SRR1552488_1.fastq FASTQ DNA 85,461,959 4,273,097,950 50 50 50
SRR1552488_2.fastq FASTQ DNA 85,461,959 4,102,174,032 48 48 48
so It can be?
--k 25,31,35 --maxReadLen 50
Selection of kmers is based on your read length. However, no matter the length, try to have a combination of "short" and "long" kmers. Short kmers generate more transcripts (but with more errors), and long kmers generate less transcripts (but with less misassemblies). For 50bp I often used --k 25,33,37
. I have colleagues that tried different combinations (e.g. 25,33,39) and the results do not change much because we are using a multi assembler approach.
The tool looks excellent, I would like to implement it in my analysis: I followed the installation tutorial, including the installation of the metazoa database, I got the following: bin docs precheck_TransPi.sh template.nextflow.config conf LICENSE README.md transpi_env.yml DBs nextflow remove_failed.sh TransPi.nf Dockerfile nextflow.config scripts update_databases.sh And when running the script with the location of my samples: nextflow run TransPi.nf --all --maxReadLen 150 --k 25,35,55,75 --reads /PATH/filter_samples/*_R[1,2].fastq.gz -profile conda --myConda The following error was reported: nextflow: command not found I would be grateful if you could please guide me in resolving the problem.
Hello @Guarup,
Did you use the precheck script? It looks like you are missing nextflow
program. I'll suggest to run the precheck again to make sure all the requirements are installed. Let me know how it goes.
Best, Ramon
Also, it could be that you have nextflow installed locally in the directory (done with the precheck) and need to add the ./
before the name to execute the program (e.g ./nextflow ...
).
Hi,
Thank you for providing such a very beneficial tool
However, I try to install the program and I faced an error while I install it, I attach the screenshot
I select EUKARYOTA, and then I select Superkingdom, suddenly the program stops with the error message above.
Here are the commands I used so far