KunFang93
commented
3 months ago Hi,
I would like to report that I encountered same error with the error below:
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS (1)'
Caused by:
Process `NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS (1)` terminated with an error exit status (1)
Command executed:
#!/usr/bin/env python
import yaml
import platform
from textwrap import dedent
def _make_versions_html(versions):
html = [
dedent(
'''\
<style>
#nf-core-versions tbody:nth-child(even) {
background-color: #f2f2f2;
}
</style>
<table class="table" style="width:100%" id="nf-core-versions">
<thead>
<tr>
<th> Process Name </th>
<th> Software </th>
<th> Version </th>
</tr>
</thead>
'''
)
]
for process, tmp_versions in sorted(versions.items()):
html.append("<tbody>")
for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
html.append(
dedent(
f'''\
<tr>
<td><samp>{process if (i == 0) else ''}</samp></td>
<td><samp>{tool}</samp></td>
<td><samp>{version}</samp></td>
</tr>
'''
)
)
html.append("</tbody>")
html.append("</table>")
return "\n".join(html)
def _make_versions_unique_html(versions):
unique_versions = []
for process, tmp_versions in sorted(versions.items()):
for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
tool_version = tool + "=" + version
if tool_version not in unique_versions:
unique_versions.append(tool_version)
unique_versions.sort()
html = [
dedent(
'''\
<style>
#nf-core-versions-unique tbody:nth-child(even) {
background-color: #f2f2f2;
}
</style>
<table class="table" style="width:100%" id="nf-core-versions-unique">
<thead>
<tr>
<th> Software </th>
<th> Version </th>
</tr>
</thead>
'''
)
]
for tool_version in unique_versions:
tool_version_split = tool_version.split('=')
html.append("<tbody>")
html.append(
dedent(
f'''\
<tr>
<td><samp>{tool_version_split[0]}</samp></td>
<td><samp>{tool_version_split[1]}</samp></td>
</tr>
'''
)
)
html.append("</tbody>")
html.append("</table>")
return "\n".join(html)
module_versions = {}
module_versions["NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS"] = {
'python': platform.python_version(),
'yaml': yaml.__version__
}
with open("versions.yml") as f:
workflow_versions = yaml.load(f, Loader=yaml.BaseLoader) | module_versions
workflow_versions["Workflow"] = {
"Nextflow": "24.04.4",
"nf-core/cutandrun": "3.2.2"
}
versions_mqc = {
'parent_id': 'software_versions',
'parent_name': 'Software Versions',
'parent_description': 'Details software versions used in the pipeline run',
'id': 'software-versions-by-process',
'section_name': 'nf-core/cutandrun software versions by process',
'section_href': 'https://github.com/nf-core/cutandrun',
'plot_type': 'html',
'description': 'are collected at run time from the software output.',
'data': _make_versions_html(workflow_versions)
}
versions_mqc_unique = {
'parent_id': 'software_versions',
'parent_name': 'Software Versions',
'parent_description': 'Details software versions used in the pipeline run',
'id': 'software-versions-unique',
'section_name': 'nf-core/cutandrun Software Versions',
'section_href': 'https://github.com/nf-core/cutandrun',
'plot_type': 'html',
'description': 'are collected at run time from the software output.',
'data': _make_versions_unique_html(workflow_versions)
}
with open("software_versions.yml", 'w') as f:
yaml.dump(workflow_versions, f, default_flow_style=False)
with open("software_versions_mqc.yml", 'w') as f:
yaml.dump(versions_mqc, f, default_flow_style=False)
with open("software_versions_unique_mqc.yml", 'w') as f:
yaml.dump(versions_mqc_unique, f, default_flow_style=False)
with open('local_versions.yml', 'w') as f:
yaml.dump(module_versions, f, default_flow_style=False)
Command exit status:
1
Command output:
(empty)
Command error:
INFO: Converting SIF file to temporary sandbox...
Traceback (most recent call last):
File ".command.sh", line 99, in <module>
workflow_versions = yaml.load(f, Loader=yaml.BaseLoader) | module_versions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/__init__.py", line 114, in load
return loader.get_single_data()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/constructor.py", line 49, in get_single_data
node = self.get_single_node()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 36, in get_single_node
document = self.compose_document()
^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 55, in compose_document
node = self.compose_node(None, None)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 133, in compose_mapping_node
item_value = self.compose_node(node, item_key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 84, in compose_node
node = self.compose_mapping_node(anchor)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/composer.py", line 127, in compose_mapping_node
while not self.check_event(MappingEndEvent):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/parser.py", line 98, in check_event
self.current_event = self.state()
^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/parser.py", line 428, in parse_block_mapping_key
if self.check_token(KeyToken):
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/scanner.py", line 116, in check_token
self.fetch_more_tokens()
File "/usr/local/lib/python3.11/site-packages/yaml/scanner.py", line 223, in fetch_more_tokens
return self.fetch_value()
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/yaml/scanner.py", line 577, in fetch_value
raise ScannerError(None, None,
yaml.scanner.ScannerError: mapping values are not allowed here
in "versions.yml", line 463, column 18
INFO: Cleaning up image...
Work dir:
/data1/kfang/HuiZ/PancreaticCancer/rawdata/work/3f/82be7eb85508142fad6afac673f30a
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command lineAnd I cannot rollback to 3.6.3 as showed
(nextflow) [kfang@zjlabs rawdata]$ mamba install -c conda-forge "singularity=3.6.3"
Looking for: ['singularity=3.6.3']
conda-forge/noarch 16.0MB @ 24.7MB/s 0.7s
conda-forge/linux-64 37.0MB @ 40.5MB/s 1.0s
Pinned packages:
- python 3.12.*
warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
├─ python is installable with the potential options
│ ├─ python 3.12.0 would require
│ │ └─ openssl >=3.1.3,<4.0a0 , which can be installed;
│ ├─ python [3.12.4|3.12.5] would require
│ │ └─ openssl >=3.3.1,<4.0a0 , which can be installed;
│ ├─ python [1.0.1|1.2|...|3.9.9], which can be installed;
│ ├─ python 3.12.0rc3 would require
│ │ └─ _python_rc, which does not exist (perhaps a missing channel);
│ ├─ python 3.12.1 would require
│ │ └─ openssl >=3.2.0,<4.0a0 , which can be installed;
│ └─ python [3.12.2|3.12.3] would require
│ └─ openssl >=3.2.1,<4.0a0 , which can be installed;
└─ singularity 3.6.3** is not installable because it requires
└─ openssl >=1.1.1g,<1.1.2a , which conflicts with any installable versions previously reported.I wondered if you could shed some light on this? Thanks a lot for helping!
Best, Kun
chris-cheshire
Description of the bug
ERROR ~ Error executing process > 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS (1)'
Seems to be when creating multiQC file? Perhaps this is due to wanting to create heatmap with all samples in deeptools?
Command used and terminal output
Relevant files
Archive 2.zip
System information
Nextflow version - version 24.04.4 build 5917 Hardware - HPC Executor - slurm Container engine - Singularity OS - Linux Version of nf-core/cutandrun - v3.2.2-g6e1125d