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l'm on a Centos HPC, so installing with the regular CentOS instruction isn´t an option for me. Unfortunately, building the singularity image gives me an array of error which I'm trying to resolve at the moment. When I use the pre-build singularity image from https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=CrisprCasFinder.simg, with this comand in a wrapper bash script
Nb of Cas in this sequence = 2
mv: cannot move 'CP014688.fna' to 'sequence_17_3_2022_7_47_18/analyzedSequences/CP014688.fna': Device or resource busy
failure: "mv CP014688.fna sequence_17_3_2022_7_47_18/analyzedSequences", errorcode 256
EDIT: after such a failed execution the result.json only consists of {
I've managed to build the image, up to the %test by applying this patch: patch.txt
patch --backup Singularity patch.txt
But then I get this error:
open : Read-only file system at /usr/local/bin/CRISPRCasFinder line 419.
Test failed see /tmp/test_CRISPRCasFinder_2022-03-17-06:50:50 for details.
FATAL: While performing build: failed to execute %test script: exit status 30
Unfortunately, I can't have a look at the mentioned /tmp/test_CRISPCasFinder_2022-03-17-06:50:50.
I had a look at line 417-420:
## JSON file "result.json"
my $jsonResult = "result.json"; # JSON result to get all info concerning CRISPR-Cas and sequences JSON files
open (JSONRES, ">$jsonResult") or die "open : $!";
print JSONRES "{\n";
Any help or tips in the right direction would be appreciated.
The text was updated successfully, but these errors were encountered:
Hi @pur80a ,
Thank you for your message. Unfortunately, I have no complete access to a CentOS machine for the moment. We will try to sole this issue as soon as possible.
The mv calls are causing issues on shared filesystems. See reports:
- dcouvin#35
- EBI-Metagenomics/mobilome-annotation-pipeline#37
This patch is not an ideal solution; the proper approach would be to avoid moving or copying files and instead
generate them directly in their final folder. However, I don't have the capacity to address this or the necessary Perl knowledge.
The container is compatible with Docker and Singularity.
l'm on a Centos HPC, so installing with the regular CentOS instruction isn´t an option for me. Unfortunately, building the singularity image gives me an array of error which I'm trying to resolve at the moment. When I use the pre-build singularity image from https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=CrisprCasFinder.simg, with this comand in a wrapper bash script
I always get the following error:
EDIT: after such a failed execution the
result.json
only consists of{
I've managed to build the image, up to the %test by applying this patch:
patch.txt
But then I get this error:
Unfortunately, I can't have a look at the mentioned
/tmp/test_CRISPCasFinder_2022-03-17-06:50:50
.I had a look at line 417-420:
Any help or tips in the right direction would be appreciated.
The text was updated successfully, but these errors were encountered: