Cumulus ADT adding spaces to file names

[Alyssa DuBois]

Hello,

I just switched to the most recent version of Cumulus on Terra and encountered an issue with generating ADT count matrices when I ran cellranger_workflow. I used the same inputs and files that I used successfully with an older version of cumulus, but this time all of my ADT count matrices failed ("Job cumulus_adt.run_generate_count_matrix_ADTs:NA:1 exited with return code 1 which has not been declared as a valid return code"). 

Looking into the logs (call-run_generate_count_matrix_ADTs/run_generate_count_matrix_ADTs.log) I think I may have found the problem. At the end of the log, the files are written with an additional space added after "citeseq" or "hashing":

Feature 'citeseq ':
SI-TN-B1.citeseq .stat.csv.gz is written.
SI-TN-B1.citeseq .csv is written.
Feature 'hashing ':
SI-TN-B1.hashing .stat.csv.gz is written.
SI-TN-B1.hashing .csv is written.

The errors after this look like:

BadRequestException: 400 Disallowed unicode characters present in object name 'Cohort3.7/Cohort3.7.1/cellranger_output_20230929/SI-TN-B1/SI-TN-B1.hashing .csv'

I have confirmed that I did not add a space after these words in my input CSVs. Do you know where else this space might be coming from?

Thank you,

Alyssa

[Yiming Yang]

Hello Alyssa,

Thanks for reaching!

May I know the version of Cumulus cellranger workflow that you used? Also, if possible, could you please share the log file of your failed job?

Sincerely,

Yiming

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