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[bug]Process BACTOPIA:ASSEMBLER:ASSEMBLER_MODULE (reads)
terminated with an error exit status (1)
#496
Comments
Can you share any more information? There should be a file called |
2024-03-22 22:18:47 - mad_joliot - 0cd9f79ba7 ec645a1e-939b-4156-9038-f8718995049e nextflow run /Users/Sauer/miniforge3/envs/bactopia//share/bactopia-3.0.0/main.nf -w /Users/Sauer/work/ --sample my-sample --SE/Users/Sauer/bactopia/Sauer_C8H_1/reads/raw_reads.fastq.gz -profile docker |
Can you share the error messages (the red text at the end of the run) or the |
Hi@rpetit3 |
How much memory do you have of your system? |
8 GB 1867 MHz DDR3 |
Do mind trying the test?
I want to verify it works here. Also, you might consider giving docker more resources: https://docs.docker.com/desktop/settings/mac/#resources |
Hi @rpetit3 |
This is making me wonder if its a "not enough memory" error you are getting. Did you try giving Docker more memory? right now it looks like 3.83GB is allocated to Docker |
Thanks @rpetit3 |
Hii @rpetit3
|
I was afraid this might happen. The test uses a super small bacterium (genome size 300,000bp) Your sample is mush larger (~5,000,000 bp), and is asking for more memory than your system has. Do you have access to another system? Or if its not too many genomes I can help with processing for you. |
Hii @rpetit3 |
No problem, if there are any questions related to setup on your hub system, please feel free to reach out to me. |
Thanks @rpetit3 |
hii@rpetit3 |
Is there any documentation about the hub, or can you give details about it? (Is it a single server or a cluster? Does it have a job scheduler (SLURM, SGE, etc..)? Does it support Docker or Singularity?) Cheers, |
It is a cluster; yes, it has a job scheduler(SLURM). I don't know about Docker or Singularity. |
It shows me that it supports docker/18.09.9 |
Check on Singularity support Do you have an example script that you would use to submit a job? |
No, I don't have any scripts right now. I am checking the documentation of the hub if they have an example |
yes they also have singularity support singularity/3.4.1 |
great, let's see if you can dig up an example script, then I think we can get something put together |
can you please have a look at them I tried looking fir the example script but it is not clear to me https://spiediedocs.binghamton.edu/docs/spiedie_modules.html |
is there a module for conda? (miniforge, conda, miniconda, etc...) |
I see only python 37 and python 39 but no conda, miniconda and miniforge |
I see miniconda in there. Here's what I'm thinking
If this works, share the |
This unfortunately might be an issue you will need to ask about. I assume your username is |
yes user name is ksauer. Do I need to ask the spiedie management about the permission to write. |
Yeah, I think the screen shot should be helpful enough for them to see what is happening |
I will talk to them about this and contact you again. |
Description
Process
BACTOPIA:ASSEMBLER:ASSEMBLER_MODULE (reads)
terminated with an error exit status (1)Steps to Reproduce
bactopia --sample reads --se fastqs/raw_reads.fastq.gz -profile docker
Expected Behavior
A description of what is expected to happen.
Execution Environment
Additional Information
Any other information you think might be helpful in squashing this bug.
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