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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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CRISPRAnalyzeR container crashing during "Check Upload" step #30

Closed deb-m closed 6 years ago

deb-m commented 6 years ago

When I am trying to test run the example data in my local installation the container is crashing asking me to reload the page. Here are my settings:-

# docker info Containers: 2 Running: 1 Paused: 0 Stopped: 1 Images: 3 Server Version: 17.09.0-ce Storage Driver: overlay2 Backing Filesystem: extfs Supports d_type: true Native Overlay Diff: true Logging Driver: json-file Cgroup Driver: cgroupfs Plugins: Volume: local Network: bridge host macvlan null overlay Log: awslogs fluentd gcplogs gelf journald json-file logentries splunk syslog Swarm: inactive Runtimes: runc Default Runtime: runc Init Binary: docker-init containerd version: 06b9cb35161009dcb7123345749fef02f7cea8e0 runc version: 3f2f8b84a77f73d38244dd690525642a72156c64 init version: 949e6fa Security Options: apparmor seccomp Profile: default Kernel Version: 4.4.0-96-generic Operating System: Ubuntu 16.04.3 LTS OSType: linux Architecture: x86_64 CPUs: 12 Total Memory: 31.32GiB Name: pje-lab ID: JB3H:RF62:6HWZ:YIXL:4TGF:2U6V:PSFD:DJFS:TGYI:DGKL:WVWP:A7TZ Docker Root Dir: /var/lib/docker Debug Mode (client): false Debug Mode (server): false Registry: https://index.docker.io/v1/ Experimental: false Insecure Registries: 127.0.0.0/8 Live Restore Enabled: false

WARNING: No swap limit support

The docker logs:-

# docker logs 6f77558... [CUSTOM] setting enhanced websocket settings [CUSTOM] setting verbose shiny server and application logfiles [CUSTOM] setting the path to the COSMIC database [CUSTOM] EnrichR interface [CUSTOM] setting the EnrichR URL [CUSTOM] Set maximum upload Size [CUSTOM] setting number of threads for Bowtie2

Any help regarding the settings or how to debug will be greatly appreciated. Thanks

jwinter6 commented 6 years ago

Hi,

thanks for your comment.

Could you please tell me the following:

In case you are at the latest, could you please go to the About CRISPRAnalyzR page and send me a screenshot and the log files (Download logfiles button) to jan.winter@dkfz-heidelberg.de?

Best, Jan

deb-m commented 6 years ago

Hi Jan, I am using latest (# docker run --rm -e bowtie_threads=2 -p 80:3838 boutroslab/crispranalyzer:latest)

I tried to reproduce the error today, and it went through without any error. I did restart the machine in between, do not know if that helped.

Thanks for your reply. Deb

deb-m commented 6 years ago

Hi Jan, After testing that the example data is uploading properly and being checked, I went ahead with 5 fastq.gz files of my experiment, and the server crashed again.

  1. I am using latest (# docker run --rm -e bowtie_threads=2 -p 80:3838 boutroslab/crispranalyzer:latest).

  2. I am sending the zipped logfile to your email address.

Thanks Deb

jwinter6 commented 6 years ago

HI Deb,

just checked the logs and it seems to be the FASTA Brunello file in the default settings which I forgot to include in the docker image.

Did the Example data work now? (so not Brunello but Example)? In the logs you sent I cannot find any crash when you used the sample data. Can you do me a favor and give it another try with the sample data? Once it crashed, close the browser, open it again and then please send me the log files from the About CRISPRAnalyzeR page.

Thanks for you help, I really appreciate it. Jan

deb-m commented 6 years ago

Hi Jan,

On Oct 4, 2017, at 12:17 PM, Jan Winter notifications@github.com wrote:

HI Deb,

just checked the logs and it seems to be the FASTA Brunello file in the default settings which I forgot to include in the docker image.

Related to this I find two names for the Brunello sgRNA library at GitHub:-

  1. At master, under the fasta dir, there is a file named “FASTA_Brunello.fasta”
  2. In README.md, under the section, "Premade sgRNA library fasta files (image), there is a “FASTA” link in the "Brunello” row, which when I click I am getting a 404 Error as it is searching for a file named “FASTA_brunello_library.fasta”.

Did the Example data work now? (so not Brunello but Example)?

The example data with example sgRNA lib is working without problem. In the logs you sent I cannot find any crash when you used the sample data.

Please disregard the logs that I sent you earlier, as it is not related to the sample data crash. Can you do me a favor and give it another try with the sample data?

Sure. Once it crashed, close the browser, open it again and then please send me the log files from the About CRISPRAnalyzeR page.

I was not able to reproduce the crash. However as per your instruction, I have attached the log after the data upload was successful (CRISPRAnalyzeR_17-10-04_15-30-46_logs.zip) as well as the success screenshots (Sample_data_success_screenshots.pdf). Thanks for you help, I really appreciate it.

Thank you! and Boutros Lab for developing such an user friendly analysis interface. Jan

Now let me explain the 2nd issue.

  1. I downloaded the "FASTA_Brunello.fasta" from "master/fasta”.
  2. In CAnalyzeR I passed on this downloaded FASTA_Brunello.fasta as a CUSTOM sgRNA library file.
  3. I uploaded 5 fastq.gz sequencing data files of my experiment.
  4. Clicked “Upload and Check files” button
  5. The data was uploaded and checked successfully.
  6. I downloaded the Readcount.zip and Sequencing_quality.html files in the next page.
  7. In the next page I setup five groups and added the readcount files to the groups.
  8. Next at the setup analysis page, I kept everything at default settings, chose gr2 vs gr5 and clicked “Start Analysis”.

The analysis did not proceed, as it complained about duplicate sgRNA identifier, please see screenshot file (Screenshot at 2017-10-04_15-45-06.png)

After this happened, I issued the following command to identify any duplicate lines.

$ wc -l FASTA_Brunello.fasta<\code> 154882 FASTA_Brunello.fasta

$ uniq FASTA_Brunello.fasta | wc -l<\code> 154882

$ awk '!a[$0]++' FASTA_Brunello.fasta | wc -l<\code> 154882

$ awk 'a[$0]++' FASTA_Brunello.fasta | wc -l<\code> 0

Seems like all lines in the FASTA_Brunello.fasta are unique.

Then what is the problem during analysis? I have attached the log file of this particular issue, please see (CRISPRAnalyzeR_17-10-04_15-46-01_logs.zip).

Any advice, will be very helpful.

Thanks Deb

jwinter6 commented 6 years ago

Hi Deb,

the different FASTA files will be gone once I update the latest version in the next days.

I will check the log what exactly is the issue, but it seems this is a coding mistake, which will be fixed in the next version.

cheers Jan

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