fMRIPrep won't generate html reports

Just finished running fmriprep for a batch of 40 subjects and noticed that all subject-specific html reports were missing. I really like these reports for quality control purposes. I tried exploring what went wrong and here’s what I found:

-got an error at the very end of the processing workflow:
(copy pasting from the end of the console outputs:)

201031-00:48:57,914 nipype.workflow IMPORTANT:
         fMRIPrep finished successfully!
201031-00:48:58,33 nipype.workflow IMPORTANT:
         Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/fmriprep/logs/
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/", line 163, in main
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/", line 534, in generate_reports
    for subject_label in subject_list
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/", line 534, in <listcomp>
    for subject_label in subject_list
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/", line 514, in run_reports
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/reports/", line 371, in generate_report
    .findall((logs_path / "CITATION.html").read_text())[0]
IndexError: list index out of range

-looks like all components of the html reports have been generated successfully
-tried rerunning for only a single subject and with --report-only flag. it threw the same error

I didn’t delete any temporary work outputs, I think they should all be there (unless fmriprep deletes older ones to free up space?)

Any help would be appreciated.

For fellow googlers who’re dealing with the same issue: deleting CITATION.html from derivatives/fmriprep/logs/ solved it for me. CITATION.html was empty for some reason. Now with the --report-only flag I’m getting the desired reports. Just make sure you don’t delete the temporary work outputs until you have generated your reports.

By the way, I’m using fMRIPrep version 20.1.2.

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