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not compatible with m1 chip mac?

Open sailseem opened this issue 3 years ago • 0 comments

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

sailseem avatar Aug 27 '21 21:08 sailseem