Closed Radek91 closed 1 year ago
Dear @Radek91 ,
Thanks for reporting this issue.
Could you please send me your env configuration (python & pandas version)?
It would be nice if I could have the first 10 lines of each of your summary files, so I can reproduce the bug.
You can also try toulligQC with our Docker image (genomicpariscentre/toulligqc:2.3):
$ docker pull genomicpariscentre/toulligqc:2.3
$ docker run -ti \
-u $(id -u):$(id -g) \
--rm \
-v /path/to/basecaller/sequencing/summary/file:/path/to/basecaller/sequencing/summary/file \
-v /path/to/basecaller/sequencing/telemetry/file:/path/to/basecaller/telemetry/summary/file \
-v /path/to/result/directory:/path/to/result/directory \
toulligqc:2.3
Best, Ali
Dear Ali,
Thank you for your fast answer.
sequencing_summary.txt barcoding_summary_pass.txt barcoding_summary_fail.txt
python --version
Python 3.8.8
pip show pandas
Name: pandas
Version: 1.2.4
I am not familiar with docker and unfortunately the document is a bit limited. How can I translate my second command to the docker image ? The paths repetitions are especially confusing.
Dear @Radek91,
As I can see, your sequencing_summary.txt is a sequencing summary file with the barcode information (it contains the barcode_arrangement
column). So, you don't need to provide a Barcoding summary file.
My suggestion is to try the following command:
toulligqc \
--force \
--report-name "$run_id" \
--barcoding \
--telemetry-source "$run_path"/fastq_hac_400/sequencing_telemetry.js \
--sequencing-summary-source "$run_path"/fastq_hac_400/sequencing_summary.txt \
--html-report-path "$run_path"/toolligqc/"$run_id"_tooligqc_"$run_id".2.html \
--data-report-path "$run_path"/toolligqc/"$run_id"_tooligqc_"$run_id".2.data \
--barcodes BC01,BC02,BC03,BC04,BC05,BC06,BC07,BC08,BC09,BC10,BC11,BC12,BC13,BC14,BC15,BC16,BC17,BC18,BC19,BC20,BC21,BC22,BC23,BC24
I hope this will help. Ali
Dear Ali,
Thank you very much for your help. This worked well :-)
I believe this may be because I used one single command to perform the demultiplexing & basecalling. Then seeing that it was not producing the barcoding outputs mentioned in your github I did it separately again, creating redundant information.
Have a nice day!
Hi!
I managed to run the latest version of toulligQC (2.3) with default guppy basecalling:
However when I ran it with the demultiplexing files I got the following error:
I did not manage to debug it myself. The links to the barcoding summary files are correct:
Any idea why this is happening ?
Thank you in advance