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not compatible with m1 chip mac? #59

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sailseem opened this issue Aug 27, 2021 · 0 comments
Open

not compatible with m1 chip mac? #59

sailseem opened this issue Aug 27, 2021 · 0 comments

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@sailseem
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executor > local (4)
executor > local (5)
executor > local (5)
[bc/96dcc6] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1 ✔
executor > local (6)
[bc/96dcc6] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1 ✔
executor > local (6)
[bc/96dcc6] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1 ✔
[ae/64b3cc] process > PREPROCESS_FULL_STACK (20191121_BRAC3438.6f.roi_1) [ 50%] 1 of 2, failed: 1, retr..
[db/52ddad] process > PREPROCESS_ILASTIK_STACK (20191121_BRAC3438.6f.roi_1) [ 50%] 1 of 2, failed: 1, retr..
[- ] process > ILASTIK -
[- ] process > SEGMENTATION -
[73/20c1b0] process > output_documentation [100%] 1 of 1 ✔
[- ] process > get_software_versions -
[0e/3d3a52] NOTE: Process PREPROCESS_ILASTIK_STACK (20191121_BRAC3438.6f.roi_1) terminated with an error exit status (139) -- Execution is retried (1)
[ad/ec9904] NOTE: Process PREPROCESS_FULL_STACK (20191121_BRAC3438.6f.roi_1) terminated with an error exit status (139) -- Execution is retried (1)
Error executing process > 'PREPROCESS_ILASTIK_STACK (20191121_BRAC3438.6f.roi_1)'

Caused by:
Process PREPROCESS_ILASTIK_STACK (20191121_BRAC3438.6f.roi_1) terminated with an error exit status (139)

executor > local (6)
[bc/96dcc6] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1 ✔
[ae/64b3cc] process > PREPROCESS_FULL_STACK (20191121_BRAC3438.6f.roi_1) [ 50%] 1 of 2, failed: 1, retr..
[db/52ddad] process > PREPROCESS_ILASTIK_STACK (20191121_BRAC3438.6f.roi_1) [100%] 2 of 2, failed: 2, retr..
[- ] process > ILASTIK -
[- ] process > SEGMENTATION -
[73/20c1b0] process > output_documentation [100%] 1 of 1 ✔
[- ] process > get_software_versions -
[0e/3d3a52] NOTE: Process PREPROCESS_ILASTIK_STACK (20191121_BRAC3438.6f.roi_1) terminated with an error exit status (139) -- Execution is retried (1)
[ad/ec9904] NOTE: Process PREPROCESS_FULL_STACK (20191121_BRAC3438.6f.roi_1) terminated with an error exit status (139) -- Execution is retried (1)
Error executing process > 'PREPROCESS_ILASTIK_STACK (20191121_BRAC3438.6f.roi_1)'

Caused by:
Process PREPROCESS_ILASTIK_STACK (20191121_BRAC3438.6f.roi_1) terminated with an error exit status (139)

Command executed:

export _JAVA_OPTIONS="-Xms3g -Xmx6g"
cellprofiler
--run-headless
--pipeline ilastik_stack_preprocessing.cppipe
--image-directory ./
--plugins-directory ./plugins
--output-directory ./ilastik_stack
--log-level DEBUG
--temporary-directory ./tmp

Command exit status:
139

Command output:
(empty)

Command error:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
JVM will be started with AWT in headless mode
Creating JVM object
Picked up _JAVA_OPTIONS: -Xms3g -Xmx6g
Signalling caller
qemu: uncaught target signal 11 (Segmentation fault) - core dumped
.command.sh: line 10: 71 Segmentation fault cellprofiler --run-headless --pipeline ilastik_stack_preprocessing.cppipe --image-directory ./ --plugins-directory ./plugins --output-directory ./ilastik_stack --log-level DEBUG --temporary-directory ./tmp

Work dir:
/Users/yangfan/Documents/nextflow/work/db/52ddadc010898629c0887645c8367c

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-[nf-core/imcyto] Pipeline completed with errors-
WARN: Killing pending tasks (1)

Dear developer,

I got error when I run nextflow run nf-core/imcyto -profile test,docker can you help me with it? Thanks in advance

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