josenimo
commented
2 months ago Just to add a bit more context. I tried running it in our HPC, with singularity and got a different error :( To be fair I don't think this is running the lastest PR changes that Jeremy staged. I think we should rather wait for those changes, and then it should be all good. For some reason, I could not run jmuhlich/mcmicro -r sample_sheet_mod, kept running into
(java) nextflow run jmuhlich/mcmicro -r sample_sheet_mod -profile test,singularity --outdir ./testoutput/
N E X T F L O W ~ version 23.10.1
Can't find git repository config file -- Repository may be corrupted: /home/jnimoca/.nextflow/assets/jmuhlich/mcmicroFull traceback of MESMER with singularity
(java) nextflow run nf-core/mcmicro -r dev -profile test,singularity --outdir ./testoutput/
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/nf-core/mcmicro` [lonely_leavitt] DSL2 - revision: 5ab80be22f [dev]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/mcmicro v2.0.0-g5ab80be
------------------------------------------------------
Core Nextflow options
revision : dev
runName : lonely_leavitt
containerEngine : singularity
launchDir : /fast/home/j/jnimoca
workDir : /fast/AG_Coscia/Jose/Nextflow/Work
projectDir : /home/jnimoca/.nextflow/assets/nf-core/mcmicro
userName : jnimoca
profile : test,singularity
configFiles :
Input/output options
input : /home/jnimoca/.nextflow/assets/nf-core/mcmicro/assets/samplesheet-test.csv
outdir : ./testoutput/
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 6.h
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/mcmicro for your analysis please cite:
* The pipeline
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/mcmicro/blob/master/CITATIONS.md
------------------------------------------------------
[- ] process > NFCORE_MCMICRO:MCMICRO:ASHLAR -
executor > local (1)
executor > local (1)
executor > local (2)
[28/d83b3b] process > NFCORE_MCMICRO:MCMICRO:ASHLAR (TEST1) [100%] 1 of 1 ✔
[c7/dda7a9] process > NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1) [ 0%] 0 of 1
[- ] process > NFCORE_MCMICRO:MCMICRO:MCQUANT -
[- ] process > NFCORE_MCMICRO:MCMICRO:MULTIQC -
ERROR ~ Error executing process > 'NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1)'
Caused by:
Process `NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1)` terminated with an error exit status (1)
Command executed:
python /usr/src/app/run_app.py mesmer --squeeze --nuclear-image TEST1.ome.tif --output-directory . --output-name mask.tif --image-mpp=0.215 --nuclear-channel 0 --compartment nuclear
cat <<-END_VERSIONS > versions.yml
"NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER":
deepcell_mesmer:: 0.4.0
END_VERSIONS
Command exit status:
1
Command output:
--no-mount strings disable one or more 'mount xxx'
options set in apptainer.conf and/or
specify absolute destination path to
disable a bind path entry, or
'bind-paths' to disable all bind
path entries.
--no-pid do not run container in a new PID
namespace
--no-privs drop all privileges from root user
in container)
--no-umask do not propagate umask to the
container, set default 0022 umask
--nv enable Nvidia support
--nvccli use nvidia-container-cli for GPU
setup (experimental)
--oom-kill-disable Disable OOM killer
-o, --overlay strings use an overlayFS image for
persistent data storage or as
read-only layer of container
--passphrase prompt for an encryption passphrase
--pem-path string enter an path to a PEM formatted RSA
key for an encrypted container
-p, --pid run container in a new PID namespace
--pids-limit int Limit number of container PIDs, use
-1 for unlimited
--rocm enable experimental Rocm support
-S, --scratch strings include a scratch directory within
the container that is linked to a
temporary dir (use -W to force location)
--security strings enable security features (SELinux,
Apparmor, Seccomp)
--sharens share the namespace and image with
other containers launched from the
same parent process
--unsquash Convert SIF file to temporary
sandbox before running
-u, --userns run container in a new user namespace
--uts run container in a new UTS namespace
-W, --workdir string working directory to be used for
/tmp, /var/tmp and $HOME (if
-c/--contain was also used)
-w, --writable by default all Apptainer containers
are available as read only. This
option makes the file system
executor > local (2)
[28/d83b3b] process > NFCORE_MCMICRO:MCMICRO:ASHLAR (TEST1) [100%] 1 of 1 ✔
[c7/dda7a9] process > NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1) [100%] 1 of 1, failed: 1 ✘
[- ] process > NFCORE_MCMICRO:MCMICRO:MCQUANT -
[- ] process > NFCORE_MCMICRO:MCMICRO:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/mcmicro] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1)'
Caused by:
Process `NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1)` terminated with an error exit status (1)
Command executed:
python /usr/src/app/run_app.py mesmer --squeeze --nuclear-image TEST1.ome.tif --output-directory . --output-name mask.tif --image-mpp=0.215 --nuclear-channel 0 --compartment nuclear
cat <<-END_VERSIONS > versions.yml
"NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER":
deepcell_mesmer:: 0.4.0
END_VERSIONS
Command exit status:
1
Command output:
--no-mount strings disable one or more 'mount xxx'
options set in apptainer.conf and/or
specify absolute destination path to
disable a bind path entry, or
'bind-paths' to disable all bind
path entries.
--no-pid do not run container in a new PID
namespace
--no-privs drop all privileges from root user
in container)
--no-umask do not propagate umask to the
container, set default 0022 umask
--nv enable Nvidia support
--nvccli use nvidia-container-cli for GPU
setup (experimental)
--oom-kill-disable Disable OOM killer
-o, --overlay strings use an overlayFS image for
persistent data storage or as
read-only layer of container
--passphrase prompt for an encryption passphrase
--pem-path string enter an path to a PEM formatted RSA
key for an encrypted container
-p, --pid run container in a new PID namespace
--pids-limit int Limit number of container PIDs, use
-1 for unlimited
--rocm enable experimental Rocm support
-S, --scratch strings include a scratch directory within
the container that is linked to a
temporary dir (use -W to force location)
--security strings enable security features (SELinux,
Apparmor, Seccomp)
--sharens share the namespace and image with
other containers launched from the
same parent process
--unsquash Convert SIF file to temporary
sandbox before running
-u, --userns run container in a new user namespace
--uts run container in a new UTS namespace
-W, --workdir string working directory to be used for
/tmp, /var/tmp and $HOME (if
-c/--contain was also used)
-w, --writable by default all Apptainer containers
are available as read only. This
option makes the file system
executor > local (2)
[28/d83b3b] process > NFCORE_MCMICRO:MCMICRO:ASHLAR (TEST1) [100%] 1 of 1 ✔
[c7/dda7a9] process > NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1) [100%] 1 of 1, failed: 1 ✘
[- ] process > NFCORE_MCMICRO:MCMICRO:MCQUANT -
[- ] process > NFCORE_MCMICRO:MCMICRO:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/mcmicro] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1)'
Caused by:
Process `NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER (TEST1)` terminated with an error exit status (1)
Command executed:
python /usr/src/app/run_app.py mesmer --squeeze --nuclear-image TEST1.ome.tif --output-directory . --output-name mask.tif --image-mpp=0.215 --nuclear-channel 0 --compartment nuclear
cat <<-END_VERSIONS > versions.yml
"NFCORE_MCMICRO:MCMICRO:DEEPCELL_MESMER":
deepcell_mesmer:: 0.4.0
END_VERSIONS
Command exit status:
1
Command output:
--no-mount strings disable one or more 'mount xxx'
options set in apptainer.conf and/or
specify absolute destination path to
disable a bind path entry, or
'bind-paths' to disable all bind
path entries.
--no-pid do not run container in a new PID
namespace
--no-privs drop all privileges from root user
in container)
--no-umask do not propagate umask to the
container, set default 0022 umask
--nv enable Nvidia support
--nvccli use nvidia-container-cli for GPU
setup (experimental)
--oom-kill-disable Disable OOM killer
-o, --overlay strings use an overlayFS image for
persistent data storage or as
read-only layer of container
--passphrase prompt for an encryption passphrase
--pem-path string enter an path to a PEM formatted RSA
key for an encrypted container
-p, --pid run container in a new PID namespace
--pids-limit int Limit number of container PIDs, use
-1 for unlimited
--rocm enable experimental Rocm support
-S, --scratch strings include a scratch directory within
the container that is linked to a
temporary dir (use -W to force location)
--security strings enable security features (SELinux,
Apparmor, Seccomp)
--sharens share the namespace and image with
other containers launched from the
same parent process
--unsquash Convert SIF file to temporary
sandbox before running
-u, --userns run container in a new user namespace
--uts run container in a new UTS namespace
-W, --workdir string working directory to be used for
/tmp, /var/tmp and $HOME (if
-c/--contain was also used)
-w, --writable by default all Apptainer containers
are available as read only. This
option makes the file system
accessible as read/write.
--writable-tmpfs makes the file system accessible as
read-write with non persistent data
(with overlay support only)
Run 'apptainer --help' for more detailed usage information.
Command error:
--no-mount strings disable one or more 'mount xxx'
options set in apptainer.conf and/or
specify absolute destination path to
disable a bind path entry, or
'bind-paths' to disable all bind
path entries.
--no-pid do not run container in a new PID
namespace
--no-privs drop all privileges from root user
in container)
--no-umask do not propagate umask to the
container, set default 0022 umask
--nv enable Nvidia support
--nvccli use nvidia-container-cli for GPU
setup (experimental)
--oom-kill-disable Disable OOM killer
-o, --overlay strings use an overlayFS image for
persistent data storage or as
read-only layer of container
--passphrase prompt for an encryption passphrase
--pem-path string enter an path to a PEM formatted RSA
key for an encrypted container
-p, --pid run container in a new PID namespace
--pids-limit int Limit number of container PIDs, use
-1 for unlimited
--rocm enable experimental Rocm support
-S, --scratch strings include a scratch directory within
the container that is linked to a
temporary dir (use -W to force location)
--security strings enable security features (SELinux,
Apparmor, Seccomp)
--sharens share the namespace and image with
other containers launched from the
same parent process
--unsquash Convert SIF file to temporary
sandbox before running
-u, --userns run container in a new user namespace
--uts run container in a new UTS namespace
-W, --workdir string working directory to be used for
/tmp, /var/tmp and $HOME (if
-c/--contain was also used)
-w, --writable by default all Apptainer containers
are available as read only. This
option makes the file system
accessible as read/write.
--writable-tmpfs makes the file system accessible as
read-write with non persistent data
(with overlay support only)
Run 'apptainer --help' for more detailed usage information.
Work dir:
/fast/AG_Coscia/Jose/Nextflow/Work/c7/dda7a931e80759de129e1ed29d37b9
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '.nextflow.log' file for details
jmuhlich
FloWuenne
Description of the bug
Running nfcore/mcmicro test locally on a macOS (m2) runs into an issue with Mesmer. Probably due to Docker container incompatibility with amd64 processing.
Command used and terminal output
Relevant files
nextflow.log
System information
Nextflow version 23.10.1 Hardware: MacBook Pro Apple M2 Pro 16Gb Memory Executor: Local Container Engine: Docker OS: Sonoma 14.0 (23A344) nfcore/mcmicro version: https://github.com/jmuhlich/mcmicro/tree/sample_sheet_mod