dockerrun_batch.sh

[Xian220]

(docker) test@jsy:/media/test/JSY_SRT2021/LTJ/P$ bash dockerrun_batch.sh /input/files/media/test/JSY_SRT2021/LTJ/P/cs2 /output/files/media/test/JSY_SRT2021/LTJ/P/cs2 /database/media/test/JSY_SRT2021/PI 30 50 500000 bash: dockerrun_batch.sh: No such file or directory

[iskoldt-X]

Hi Xiao220,

Thank you for reaching out!

The error you're encountering often indicates that the dockerrun_batch.sh script cannot be found in your current directory. To ensure you have this file, you can download it directly from our GitHub repository using this command:

wget https://github.com/nekokoe/Plasmer/raw/main/dockerrun_batch.sh

Remember, this script needs to be in the same directory where you're trying to run the command.

Additionally, it seems there might be a misunderstanding regarding the usage of dockerrun_batch.sh. The first two arguments should be the input and output directories respectively.

Therefore, I suggest creating a new directory for your output files:

mkdir /media/test/JSY_SRT2021/LTJ/P/cs2/Plasmer-test

Then, try running the script with this command:

bash dockerrun_batch.sh /media/test/JSY_SRT2021/LTJ/P/cs2 /media/test/JSY_SRT2021/LTJ/P/cs2/Plasmer-test /media/test/JSY_SRT2021/PI 30 50 500000

This should process all files in the cs2 directory and output the results into the Plasmer-test directory.

Let us know if you need any further assistance!

[Xian220]

Thank you very much for your answer, I solved the problem.

But I found another problem, like the last one. Some output files are blank. Is this because it is not recognized? When I take a whole big file as input file, the output file is blank. When I split the large file into smaller files for input, some have results and some are still blank, and it has nothing to do with the file size. There is no pattern at all, and this is driving me crazy.

[Xian220]

I tried the format of both input files and both report the same error.

[Xian220]

Here is my code and the database I compared it to.

[Xian220]

I tried again, some can run twenty contigs at once and produce results, while some can even only run one at a time to produce results. This is too torturous.