Error during Dropseq_workflow Run on Cumulus
Hi,
I am running dropseq_workflow snapshot 6 on cumulus on some FASTQ samples that I have. In the past, we have run multiple jobs of this workflow successfully without any error. However, since around New Year, I couldn't go through with it.
I've tested using the exact same inputs (I had run successfully before) and created a new workspace to test the workflow but neither worked.
The dropseq_workflow jobs ended in the first step and here is a screenshot of the error:
It seems that there is a parsing error in the first step generate_count_config. And here is the backend log for this step:
call-generate_count_config/generate_count_config.log
2020/01/27 19:45:48 Starting container setup.
2020/01/27 19:45:51 Done container setup.
2020/01/27 19:45:52 Starting localization.
2020/01/27 19:46:12 Localization script execution started...
2020/01/27 19:46:12 Localizing input gs://regev-lab/resources/DropSeq/index.json -> /cromwell_root/regev-lab/resources/DropSeq/index.json
2020/01/27 19:46:15 Localizing input gs://fc-69be09e5-591e-47a0-8616-dd12affc2897/fef73b70-46bd-452b-ac67-099ef2dc5446/dropseq_workflow/8665c92d-84cd-42e1-8239-fd3e17a4c214/call-generate_count_config/script -> /cromwell_root/script
2020/01/27 19:46:18 Localizing input gs://fc-69be09e5-591e-47a0-8616-dd12affc2897/Seqwell_Oct_V2/samples_sheep.txt -> /cromwell_root/fc-69be09e5-591e-47a0-8616-dd12affc2897/Seqwell_Oct_V2/samples_sheep.txt
2020/01/27 19:46:20 Localization script execution complete.
2020/01/27 19:46:23 Done localization.
2020/01/27 19:46:24 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint= cumulusprod/dropseq@sha256:cb6ebd217ebb1b75e8ce685a8c0f514a183fe385bc1f5f19a40d47713dd67646 /bin/bash /cromwell_root/script
Traceback (most recent call last):
File "<stdin>", line 14, in <module>
File "/opt/conda/lib/python3.7/site-packages/pandas/io/parsers.py", line 685, in parser_f
return _read(filepath_or_buffer, kwds)
File "/opt/conda/lib/python3.7/site-packages/pandas/io/parsers.py", line 463, in _read
data = parser.read(nrows)
File "/opt/conda/lib/python3.7/site-packages/pandas/io/parsers.py", line 1154, in read
ret = self._engine.read(nrows)
File "/opt/conda/lib/python3.7/site-packages/pandas/io/parsers.py", line 2493, in read
alldata = self._rows_to_cols(content)
File "/opt/conda/lib/python3.7/site-packages/pandas/io/parsers.py", line 3157, in _rows_to_cols
self._alert_malformed(msg, row_num + 1)
File "/opt/conda/lib/python3.7/site-packages/pandas/io/parsers.py", line 2914, in _alert_malformed
raise ParserError(msg)
pandas.errors.ParserError: Expected 7 fields in line 3, saw 13
2020/01/27 19:46:37 Starting delocalization.
2020/01/27 19:46:38 Delocalization script execution started...
2020/01/27 19:46:38 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-69be09e5-591e-47a0-8616-dd12affc2897/fef73b70-46bd-452b-ac67-099ef2dc5446/dropseq_workflow/8665c92d-84cd-42e1-8239-fd3e17a4c214/call-generate_count_config/memory_retry_rc
2020/01/27 19:46:38 Delocalizing output /cromwell_root/rc -> gs://fc-69be09e5-591e-47a0-8616-dd12affc2897/fef73b70-46bd-452b-ac67-099ef2dc5446/dropseq_workflow/8665c92d-84cd-42e1-8239-fd3e17a4c214/call-generate_count_config/rc
2020/01/27 19:46:39 Delocalizing output /cromwell_root/stdout -> gs://fc-69be09e5-591e-47a0-8616-dd12affc2897/fef73b70-46bd-452b-ac67-099ef2dc5446/dropseq_workflow/8665c92d-84cd-42e1-8239-fd3e17a4c214/call-generate_count_config/stdout
2020/01/27 19:46:41 Delocalizing output /cromwell_root/stderr -> gs://fc-69be09e5-591e-47a0-8616-dd12affc2897/fef73b70-46bd-452b-ac67-099ef2dc5446/dropseq_workflow/8665c92d-84cd-42e1-8239-fd3e17a4c214/call-generate_count_config/stderr
2020/01/27 19:46:42 Delocalizing output /cromwell_root/refflat.txt -> gs://fc-69be09e5-591e-47a0-8616-dd12affc2897/fef73b70-46bd-452b-ac67-099ef2dc5446/dropseq_workflow/8665c92d-84cd-42e1-8239-fd3e17a4c214/call-generate_count_config/refflat.txt
Required file output '/cromwell_root/refflat.txt' does not exist.
I'm wondering if anybody has seen this error before or how to resolve it?
Thank you,
Hanbing Song
Comments
3 comments
Hi Hanbing,
Thank you for reporting the error, we'll be happy to take a closer look. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in either the icon of your workspace in the workspace list or inside the workspace dashboard (see the icon with the three dots). Let us know the workspace name, as well as the relevant submission and workflow ID(s).
Kind regards,
Jason
Hi Jason,
Thanks for following up on this. I talked to Dr. Josh Gould who made the dropseq_workflow and he helped me figure out the problem. The input sample list should be comma-delimited. But in the past I've been using tab-delimited file, which caused the parsing error. Now I changed the input sample list to comma-delimited and the error is gone.
Hanbing
Hi Hanbing,
Sounds good—glad to to hear you were able to get it working! If we can be of any further assistance, please let us know.
Kind regards,
Jason
Please sign in to leave a comment.