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running quickstart tutorial fails: squashfs-tools not available #102
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Thanks @stephenturner. This seems to be related to apptainer/singularity#1078. Does installing |
Just skimmed through that issue, it's not clear how to install @stephenturner is this on Ravenna/HPC or your local machine? |
Gotcha, on ubuntu |
Local. Centos7.
…On Wed, Jul 11, 2018 at 2:14 PM Phillip Brooks ***@***.***> wrote:
Gotcha, on ubuntu sudo apt-get install squashfs-tools.
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Installed with `sudo yum install squashfs-tools`, but after that:
```
Job 1: --- Pre-trim quality check of trimmed data with fastqc.
fastqc -t 1 //data/SRR606249_subset10_1_reads.fq.gz
/data/SRR606249_subset10_2_reads.fq.gz -o /data
Activating singularity image
/nv/vol184/uvabx/projects/dahak/dahak/workflows/.snakemake/singularity/f1d03c0a142609dc68fd5a6943abcaad.simg
ERROR : Failed invoking the NEWUSER namespace runtime: Invalid argument
ABORT : Retval = 255
Error in rule pre_trimming_quality_assessment:
jobid: 1
output: data/SRR606249_subset10_1_reads_fastqc.zip,
data/SRR606249_subset10_2_reads_fastqc.zip
RuleException:
CalledProcessError in line 162 of
/nv/vol184/uvabx/projects/dahak/dahak/workflows/read_filtering/Snakefile:
Command 'singularity exec --home
/nv/vol184/uvabx/projects/dahak/dahak/workflows
/nv/vol184/uvabx/projects/dahak/dahak/workflows/.snakemake/singularity/f1d03c0a142609dc68fd5a6943abcaad.simg
bash -c " set -euo pipefail; fastqc -t 1
//data/SRR606249_subset10_1_reads.fq.gz
/data/SRR606249_subset10_2_reads.fq.gz -o /data "' returned non-zero exit
status 255.
File
"/nv/vol184/uvabx/projects/dahak/dahak/workflows/read_filtering/Snakefile",
line 162, in __rule_pre_trimming_quality_assessment
File
"/home/sdt5z/miniconda3/envs/dahak/lib/python3.6/concurrent/futures/thread.py",
line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log:
/nv/vol184/uvabx/projects/dahak/dahak/workflows/.snakemake/log/2018-07-11T161047.251072.snakemake.log
```
…On Wed, Jul 11, 2018 at 4:09 PM Stephen Turner ***@***.***> wrote:
Local. Centos7.
On Wed, Jul 11, 2018 at 2:14 PM Phillip Brooks ***@***.***>
wrote:
> Gotcha, on ubuntu sudo apt-get install squashfs-tools.
>
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> <#102 (comment)>,
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This issue was raised in the singularity repo here, problem was with RedHat. It sounds like a problem with Linux and Singularity not playing nicely together. I am currently working on reproducing this error on an AWS node running CentOS.... |
We've previously had trouble getting that FastQC docker to run on Red Hat, and it may be a Fedora compatibility issue. Is it possible for @stephenturner to skip that step and test the next step in the workflow to narrow down whether it's an issue with the FastQC container or something else? |
RHEL/Fedora/CentOS should all be the same, essentially. The assembly quickstart (https://dahak-metagenomics.github.io/dahak/quickstart/#assembly) has the same issue as noted above. After creating the json file, and running:
Get the same NEWUSER/namespace problem:
|
Thanks for sharing that! I was going to ask @nalbright try different workflow steps on Red Hat, but it looks like that wouldn't be helpful based on your experience here. We can setup an Ubuntu OS for testing, and I'll have her focus on that for now. |
Hi @kternus, yes, this is a generic problem with RedHat and Singularity. |
@stephenturner This has some resources we may been to reference: |
I wasn't able to get |
So, I did that, and I'm getting past the NEWUSER error but hitting a wall with
I googled around a bit and landed on a few issues on the singularity repo, but nothing I could grok. I do have squashfs-tools installed. |
Should also add
|
When I was getting the squashfs errors on centos I had to rerun the configure command after I installed the package. But it sounds like you have installed the package then run the configure command.
From: Stephen Turner <notifications@github.com>
Sent: Wednesday, July 18, 2018 2:57 PM
To: dahak-metagenomics/dahak <dahak@noreply.github.com>
Cc: Grahlmann, Chris <cgrahlmann@signaturescience.com>; Comment <comment@noreply.github.com>
Subject: Re: [dahak-metagenomics/dahak] running quickstart tutorial fails: squashfs-tools not available (#102)
Should also add
$ singularity --version
2.5.2-dist
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Precisely
Stephen
Sent from mobile.
… On Jul 18, 2018, at 4:26 PM, cgrahlma ***@***.***> wrote:
When I was getting the squashfs errors on centos I had to rerun the configure command after I installed the package. But it sounds like you have installed the package then run the configure command.
From: Stephen Turner ***@***.***>
Sent: Wednesday, July 18, 2018 2:57 PM
To: dahak-metagenomics/dahak ***@***.***>
Cc: Grahlmann, Chris ***@***.***>; Comment ***@***.***>
Subject: Re: [dahak-metagenomics/dahak] running quickstart tutorial fails: squashfs-tools not available (#102)
Should also add
$ singularity --version
2.5.2-dist
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Trying to run the read filtering workflow at https://dahak-metagenomics.github.io/dahak/quickstart/#read-filtering
After setting up the environment as noted in #99 and issuing the following command (with
--use-singularity
):I get:
Please provide further installation/setup instructions.
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