[GENERAL] Error in process_sample_file: 'NoneType' object is not iterable

[senzhaocode]

⚠️ Reminder

ROBIN is developed for RESEARCH USE ONLY.

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📝 Description

2025-09-21 12:14:19,390 - 100t - ERROR - Error in process_sample_files: 'NoneType' object is not iterable
Traceback (most recent call last) :
File "/cluster/work/users/senz/ROBIN-dev/src/robin/brain_class.py", line 3277, in process_sample_files dict(self.mnpflex_config),
TypeError: 'NoneType'
object is not iterable
2025-09-21 12:14:19,392 - root - ERROR - Error updating failed counters for NANODX: 'bams_failed'
2025-09-21 12:14:19,392 - root - ERROR - Error updating failed counters for PANNANODX: 'bams_failed'
2025-09-21 12:14:19,392 - 10ot - ERROR - Error updating failed counters for FOREST: 'bams_failed'
2025-09-21 12:14:19,393 - nicegui - ERROR - 'NoneType' object is not iterable
Traceback (most recent call last) :
File "/cluster/home/senz/.conda/envs/robin_0_3/1ib/python3.9/site-packages/nicegui/timer.py", line 110, in _invoke_callback await result
File "/cluster/work/users/senz/ROBIN-dev/src/robin/brain_class.py", line 3059, in process_bigbadmerge await self.process_sample_files(
File "/cluster/work/users/senz/ROBIN-dev/src/robin/brain_class.py", line 3277, in process_sample_files dict(self.mnpflex_config),
TypeError: 'NoneType' object is not iterable

❓ Context

This error occurs when importing BAM files from ROBIN_test_set_A for a testing run. It looks BAM files are loaded not completely and Robin can not run properly.

🔧 Steps Taken

List any actions or investigations you have already performed to address or understand this issue:

• ROBIN Version: dev branch
• Operating System: Linux CentOS 8

Attached a command line parameters that were used for running

echo "I agree" | robin --threads 32 --showerrors \
	-r /data/senz/reference/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta \
	-b /data/senz/ROBIN-dev/src/robin/resources/panel_11092024_5kb_pad.bed \
	-e coverage \
	-e mgmt \
	-e sturgeon \
	--centreid IPDtest \
	--log-file /data/senz/analysis.log \
	--log-level INFO \
	--basecall_config "dorado" \
	--experiment_duration 72 \
	--enable-snp-calling \
	-w /data/senz/ROBIN_test_set_A/test_data_set /data/senz/ROBIN_output

🌟 Expected Outcome

This issue needs to be fixed before robin can completely the whole analysis.

📸 Additional Information

Attached a a screenshot where robin got stuck.

⚙️ Suggestions or Feedback

Could you have a look and fix it. Many thanks in advance