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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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aucell returns EOF error #122

Closed TsumaR closed 3 years ago

TsumaR commented 4 years ago

Hi,

I am trying to run aucell. I use your docker image by singularity, but I got a EOF error. pyscenic grn and pyescnic ctx did well.

command

singularity run aertslab-pyscenic-0.9.19.sif \
  pyscenic aucell \
  count.tsv \
  regulons.csv \
  -o auc_mtx.csv \
  --num_workers 6

Then, I got the below error message.

/bin/bash: /home/myne812/anaconda3/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/opt/venv/lib/python3.7/site-packages/dask/config.py:161: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  data = yaml.load(f.read()) or {}

2019-12-26 14:42:13,675 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2019-12-26 14:42:15,036 - pyscenic.cli.pyscenic - INFO - Loading gene signatures.

2019-12-26 14:42:15,053 - pyscenic.cli.pyscenic - ERROR - Error tokenizing data. C error: EOF inside string starting at row 52

regulons.csv file

image

Please help

"Postscripts" The file ended unexpectedly and was not output to the end. The core file was output.

cflerin commented 4 years ago

Hi, the screenshot you posted looks like it's from excel, or a similar program. Is it possible that excel over-wrote the regulons.csv with its own format? This would certainly cause a problem when trying to read the file back in at the AUCell step.