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boutroslab / CRISPRAnalyzeR

CRISPRAnalyzeR: interactive analysis, annotation and documentation of pooled CRISPR screens
GNU General Public License v2.0
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docker container & fastq #59

Open chrispam416 opened 5 years ago

chrispam416 commented 5 years ago

Hi,

We have been trying to use CRISPRAnalyzer to analyze NGS data from a GECKO assay. We are having trouble uploading the raw FastQ files which are in the format of .fastq.gz (GZIP-compressed). The program loads well for files up to 1.7 GB, but our computer crashes for files >1.7 GB. However, there is no problem with uploading of the readcount files in .txt format and aligning it against the reference GECKO library. Have anyone encountered the same problem as us? Is there any way to increase the upload size limit of FastQ files beyond 1.7 GB?

Otherwise, is there an alternative way to generate the readcounts in text format without having to upload the files in the GZIP-compressed format? Do you have any recommendations for the computer specifications that is best for running the software?

We're using 64 Gb, Ubuntu 18.04.2 LTS currently.

Also, how do we obtain the log files for this docker container? There are a few couple issues with the container recently where it seems like the container has been inactivated where we get this error message: Cannot connect to the docker daemon at unix ///var/run/docker.sock is the docker daemon running?

Thanks! Chris

EdGreen21 commented 5 years ago

https://github.com/boutroslab/CRISPRAnalyzeR/issues/18

EdGreen21 commented 5 years ago

you need to increase file limits, see fix above

chrispam416 commented 5 years ago

Hi, I've tried increasing the file limits with the following:

docker run -e max_upload=8096 --memory="40g" --memory-swap="80g" --rm -p 8000:8000 boutroslab/crispranalyzer:latest

but whenever it's uploading, the program crashes.

Is there any way to obtain any debug files here?