Open guijie2015 opened 3 days ago
Hi, and thanks for the very detailed report.
We have noticed this issue in the spacemake automated_analysis
, and a bugfix is in progress.
For the rest of the Open-ST workflow, these reports are not really necessary. You can make sure the rest of the pipeline runs by using --keep_going
flag in spacemake.
I hope this helps, and sorry for the inconvenience!
Dani
Hi, and thanks for the very detailed report.
We have noticed this issue in the spacemake
automated_analysis
, and a bugfix is in progress.For the rest of the Open-ST workflow, these reports are not really necessary. You can make sure the rest of the pipeline runs by using
--keep_going
flag in spacemake.I hope this helps, and sorry for the inconvenience!
Dani
Very thanksful for your reply. But I am very sorry fot that when I am trying using '--keep_going' and then running the next step Pairwise alignment. It told me I miss the dge.all.polyA_adapter_trimmed.mm_included.spatial_beads_puck_collection.h5ad file.
How can I create this dge.all.polyA_adapter_trimmed.mm_included.spatial_beads_puck_collection.h5ad.
Here is my Pairwise alignment code. openst from_spacemake --project-id openst_demo --sample-id openst_demo_e13_mouse_head merge_modalities
That probably means you used the default spacemake mode that runs meshing before stitching the puck_collection
, therefore that file will not be available. You have to generate it using openst from_spacemake ... spatial_stitch
, take a look here:
https://rajewsky-lab.github.io/openst/latest/computational/pairwise_alignment/#tissue-transcriptome
Under "My run_mode
and/or puck
do not look like that"
spatial_stitch
Very thanksful for your reply.
I try running these code
openst from_spacemake --project-id openst_demo\ --sample-id openst_demo_e13_mouse_head\ spatial_stitch\ --tile-coordinates fc_1_coordinate_system.csv
then get this error.
under my dge directory,I have these files. I can`t find "fc_1_tile_2267.h5ad dge.fc_1_tile_2268.h5ad", which is running spatial_stitch in manual on the example
Hi,when I`m running example data on the Preprocessing transcriptomic library step, I encounter the problem.
Here is the log file. log.log
I understand you're busy, but if you have some time, I would really appreciate your help with this issue.
Steps to reproduce the bug
Environment info
aiobotocore 2.5.4 aioeasywebdav 2.4.0 aiohappyeyeballs 2.4.3 aiohttp 3.10.10 aioitertools 0.12.0 aiosignal 1.3.1 alabaster 0.7.16 amply 0.1.6 anndata 0.10.9 annotated-types 0.7.0 appdirs 1.4.4 array_api_compat 1.9 asciitree 0.3.3 asttokens 2.4.1 async-timeout 4.0.3 attmap 0.13.2 attrs 24.2.0 babel 2.16.0 bcrypt 4.2.0 beautifulsoup4 4.12.3 bio 1.6.2 biopython 1.84 biothings-client 0.3.1 bleach 6.1.0 boto3 1.35.39 botocore 1.31.17 Brotli 1.1.0 cachetools 5.5.0 cellpose 3.0.11 certifi 2024.8.30 cffi 1.17.1 charset-normalizer 3.4.0 click 8.1.7 cloudpickle 3.1.0 colorama 0.4.6 colorcet 3.1.0 coloredlogs 15.0.1 comm 0.2.2 commonmark 0.9.1 ConfigArgParse 1.7 connection-pool 0.0.3 contourpy 1.3.0 cryptography 43.0.1 cycler 0.12.1 dask 2024.8.0 dask-expr 1.1.10 dask-image 2024.5.3 datashader 0.16.3 datrie 0.8.2 debugpy 1.8.7 decorator 5.1.1 defusedxml 0.7.1 distributed 2024.8.0 dnaio 1.2.2 docrep 0.3.2 docutils 0.21.2 dpath 2.2.0 dropbox 12.0.2 eido 0.2.2 exceptiongroup 1.2.2 executing 2.1.0 fasteners 0.19 fastjsonschema 2.20.0 fastremap 1.15.0 filechunkio 1.8 filelock 3.16.1 fonttools 4.54.1 frozenlist 1.4.1 fsspec 2023.6.0 ftputil 5.1.0 geopandas 1.0.1 get-annotations 0.1.2 ghp-import 2.1.0 gitdb 4.0.11 GitPython 3.1.43 google-api-core 2.21.0 google-api-python-client 2.149.0 google-auth 2.35.0 google-auth-httplib2 0.2.0 google-cloud-core 2.4.1 google-cloud-storage 2.18.2 google-crc32c 1.1.2 google-resumable-media 2.7.2 googleapis-common-protos 1.65.0 gprofiler-official 1.0.0 grpcio 1.46.3 h5py 3.12.1 httplib2 0.22.0 humanfriendly 10.0 idna 3.10 igraph 0.11.6 imagecodecs 2024.9.22 imageio 2.35.1 imagesize 1.4.1 importlib_metadata 8.4.0 importlib_resources 6.4.5 inflect 7.4.0 iniconfig 2.0.0 ipykernel 6.29.5 ipython 8.18.1 isal 1.7.1 jedi 0.19.1 Jinja2 3.1.4 jmespath 1.0.1 joblib 1.4.2 jsonschema 4.23.0 jsonschema-specifications 2024.10.1 jupyter_client 8.6.3 jupyter_core 5.7.2 jupyterlab_pygments 0.3.0 kiwisolver 1.4.7 kornia 0.7.3 kornia_rs 0.1.5 lazy_loader 0.4 legacy-api-wrap 1.4 leidenalg 0.10.2 llvmlite 0.43.0 locket 1.0.0 logmuse 0.2.8 Markdown 3.7 markdown-it-py 3.0.0 MarkupSafe 3.0.1 matplotlib 3.6.0 matplotlib-inline 0.1.7 matplotlib-scalebar 0.8.1 mdurl 0.1.2 mergedeep 1.3.4 mistune 3.0.2 mkdocs 1.6.1 mkdocs-autorefs 1.2.0 mkdocs-get-deps 0.2.0 mkdocs-material 9.5.40 mkdocs-material-extensions 1.3.1 mknotebooks 0.8.0 more-itertools 10.5.0 mpmath 1.3.0 msgpack 1.1.0 multidict 6.1.0 multipledispatch 1.0.0 multiscale_spatial_image 1.0.1 munkres 1.1.4 mygene 3.2.2 natsort 8.4.0 nbclient 0.10.0 nbconvert 7.16.4 nbformat 5.10.4 nest-asyncio 1.6.0 networkx 3.2.1 novosparc 0.4.4 numba 0.60.0 numcodecs 0.12.1 numpy 1.26.4 nvidia-cublas-cu12 12.1.3.1 nvidia-cuda-cupti-cu12 12.1.105 nvidia-cuda-nvrtc-cu12 12.1.105 nvidia-cuda-runtime-cu12 12.1.105 nvidia-cudnn-cu12 9.1.0.70 nvidia-cufft-cu12 11.0.2.54 nvidia-curand-cu12 10.3.2.106 nvidia-cusolver-cu12 11.4.5.107 nvidia-cusparse-cu12 12.1.0.106 nvidia-nccl-cu12 2.20.5 nvidia-nvjitlink-cu12 12.6.77 nvidia-nvtx-cu12 12.1.105 oauth2client 4.1.3 ome-zarr 0.9.0 omnipath 1.0.8 opencv-python 4.10.0.84 opencv-python-headless 4.10.0.84 openst 0.2.1 /home/data/hejunjie/software/openst packaging 24.1 paginate 0.5.7 pandas 2.2.3 pandocfilters 1.5.1 param 2.1.1 paramiko 3.5.0 parso 0.8.4 partd 1.4.2 pathspec 0.12.1 patsy 0.5.6 pephubclient 0.4.4 peppy 0.40.7 pexpect 4.9.0 Pillow 10.0.1 PIMS 0.7 pip 24.2 pkgutil_resolve_name 1.3.10 plac 1.4.3 platformdirs 4.3.6 pluggy 1.5.0 ply 3.11 pooch 1.8.2 POT 0.9.4 prettytable 3.11.0 prompt_toolkit 3.0.48 propcache 0.2.0 proto-plus 1.24.0 protobuf 5.28.2 psutil 6.0.0 ptyprocess 0.7.0 PuLP 2.7.0 pure_eval 0.2.3 pyarrow 17.0.0 pyasn1 0.6.1 pyasn1_modules 0.4.1 pycparser 2.22 pyct 0.5.0 pydantic 2.9.2 pydantic_core 2.23.4 Pygments 2.18.0 pygraphviz 1.11 pymdown-extensions 10.11.2 PyNaCl 1.5.0 pynndescent 0.5.13 pyogrio 0.10.0 pyOpenSSL 24.2.1 pyparsing 3.2.0 pyproj 3.6.1 PyQt5 5.15.9 PyQt5-Qt5 5.15.2 PyQt5-sip 12.12.2 pyqtgraph 0.13.7 pysam 0.22.1 pysftp 0.2.9 PySocks 1.7.1 pytest 8.3.3 python-dateutil 2.9.0 python-irodsclient 2.1.0 pytz 2024.1 pyu2f 0.1.5 PyWavelets 1.6.0 PyYAML 6.0.2 pyyaml_env_tag 0.1 pyzmq 26.2.0 ratelimiter 1.2.0 recommonmark 0.7.1 referencing 0.35.1 regex 2024.9.11 requests 2.32.3 reretry 0.11.8 rich 13.9.2 roifile 2024.9.15 rpds-py 0.20.0 rsa 4.9 s3fs 2023.6.0 s3transfer 0.10.3 scanpy 1.10.3 scikit-image 0.19.3 scikit-learn 1.5.2 scipy 1.13.1 seaborn 0.13.2 session_info 1.0.0 setuptools 75.1.0 shapely 2.0.6 shellingham 1.5.4 six 1.16.0 slacker 0.14.0 slicerator 1.1.0 smart_open 7.0.5 smmap 5.0.0 snakemake 6.3.0 snowballstemmer 2.2.0 sortedcontainers 2.4.0 soupsieve 2.6 spacemake 0.7.9 spatial_image 1.1.0 spatialdata 0.2.3 Sphinx 7.4.7 sphinxcontrib-applehelp 2.0.0 sphinxcontrib-devhelp 2.0.0 sphinxcontrib-htmlhelp 2.1.0 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 2.0.0 sphinxcontrib-serializinghtml 2.0.0 squidpy 1.2.1 stack-data 0.6.3 statsmodels 0.14.4 stdlib-list 0.10.0 stone 3.3.2 stopit 1.1.2 sympy 1.13.3 tabulate 0.9.0 tblib 3.0.0 texttable 1.7.0 threadpoolctl 3.5.0 throttler 1.2.2 tifffile 2024.8.30 tinycss2 1.3.0 tomli 2.0.2 toolz 1.0.0 toposort 1.10 torch 2.4.1 tornado 6.4.1 tqdm 4.66.5 traitlets 5.14.3 triton 3.0.0 typeguard 4.3.0 typer 0.12.5 typing_extensions 4.12.2 tzdata 2024.2 ubiquerg 0.8.0 umap-learn 0.5.6 unicodedata2 15.1.0 uritemplate 4.1.1 urllib3 1.26.19 validators 0.34.0 veracitools 0.1.3 watchdog 5.0.3 wcwidth 0.2.13 webencodings 0.5.1 wheel 0.44.0 wrapt 1.16.0 xarray 2024.7.0 xarray-dataclasses 1.8.0 xarray-datatree 0.0.14 xarray-schema 0.0.3 xarray-spatial 0.4.0 xopen 2.0.2 yarl 1.14.0 yte 1.5.4 zarr 2.18.2 zict 3.0.0 zipp 3.20.2 zlib-ng 0.5.1