problem with the test case
DavidSriker opened this issue · 0 comments
DavidSriker commented
I try to use the tool with the test case but I got the following error (which refers to the 20191121_BRAC3438.6f.mcd)
>>> nextflow run nf-core/imcyto -profile test,docker
N E X T F L O W ~ version 20.10.0
Launching `nf-core/imcyto` [marvelous_bhabha] - revision: b5877ce63f [master]
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,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/imcyto v1.0.0
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Run Name : marvelous_bhabha
Input Files : https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/inputs/20191121_BRAC3438.6f.mcd
Metadata File : https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/inputs/metadata.csv
Full Stack cppipe File : https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/full_stack_preprocessing.cppipe
Ilastik Stack cppipe File: https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/ilastik_stack_preprocessing.cppipe
Skip Ilastik Step : No
Ilastik Training ilp File: https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/ilastik_training_params.ilp
Segmentation cppipe File : https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/segmentation.cppipe
Max Resources : 6 GB memory, 2 cpus, 12h time per job
Container : docker - [:]
Output Dir : ./results
Launch Dir : /home/nucleai
Working Dir : /home/nucleai/work
Script Dir : /home/nucleai/.nextflow/assets/nf-core/imcyto
User : nucleai
Config Profile : test,docker
Config Description : Minimal test dataset to check pipeline function
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executor > local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [ 0%] 0 of 1
executor > local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1, failed: 1 ✘
[- ] process > PREPROCESS_FULL_STACK -
executor > local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1, failed: 1 ✘
[- ] process > PREPROCESS_FULL_STACK -
executor > local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1, failed: 1 ✘
[- ] process > PREPROCESS_FULL_STACK -
[- ] process > PREPROCESS_ILASTIK_STACK -
executor > local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1, failed: 1 ✘
[- ] process > PREPROCESS_FULL_STACK -
[- ] process > PREPROCESS_ILASTIK_STACK -
[- ] process > ILASTIK -
[- ] process > SEGMENTATION -
[d4/a4bba6] process > output_documentation [100%] 1 of 1 ✔
[- ] process > get_software_versions -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/imcyto] Pipeline completed with errors-
Error executing process > 'IMCTOOLS (20191121_BRAC3438.6f)'
Caused by:
Process `IMCTOOLS (20191121_BRAC3438.6f)` terminated with an error exit status (1)
Command executed:
run_imctools.py 20191121_BRAC3438.6f.mcd metadata.csv
pip show imctools | grep "Version" > imctools_version.txt
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/home/nucleai/.nextflow/assets/nf-core/imcyto/bin/run_imctools.py", line 73, in <module>
parser = mcdparser.McdParser(args.INPUT_FILE)
File "/usr/local/lib/python3.8/site-packages/imctools/io/mcdparser.py", line 31, in __init__
McdParserBase.__init__(self, filename, filehandle, metafilename)
File "/usr/local/lib/python3.8/site-packages/imctools/io/mcdparserbase.py", line 48, in __init__
self.retrieve_mcd_xml()
File "/usr/local/lib/python3.8/site-packages/imctools/io/mcdparser.py", line 73, in retrieve_mcd_xml
raise ValueError('Invalid MCD: MCD xml start tag not found in file %s' % self.filename)
ValueError: Invalid MCD: MCD xml start tag not found in file 20191121_BRAC3438.6f.mcd
Work dir:
/home/nucleai/work/2e/3d50156173d45bbca8d5be8dae1dd3
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Can you please suggest a way of fixing it?
Thanks