Example:
mica local -b 10 -i /Users/lding/OneDrive - St. Jude Children's Research Hospital/Projects/scMINER/bluesky_eval/src/PBMC12k_MICA_input.txt -p PBMC12k -k 8 9 10 12 13 14 15 -o /Users/lding/OneDrive - St. Jude Children's Research Hospital/Projects/scMINER/bluesky_eval/src -b 10 -dr MDS -v tsne -pp 30 -d 0.01 -sn 1000

Hi i met following error when i run MICA:

(omicverse6) root@jiang:/home/jzhou/MICA/MICA/bin# mica mds -i /mnt/c/@@@@@@@@TCF1_T_scATAC/new/CD8TMICA.h5ad -o /mnt/c/@@@@@@@@TCF1_T_scATAC/new/ -pn TRAMP -nc 16
INFO:root:Start MDS mode...
INFO:root:/mnt/c/@@@@@@@@TCF1_T_scATAC/new/mica.yml
INFO:root:infile:
class: File
path: /mnt/c/@@@@@@@@TCF1_T_scATAC/new/CD8TMICA.h5ad
project_name: TRAMP
k: [16]
num_neighbor: None
visualization: UMAP
dim_reduction: MDS
iterations_km: 10
dims_km: [19]
dims: 19
dims_plot: 19
perplexity: 30
min_dist: 0.6
slice_size: 1000
thread_number: 10
dist_metrics: mi

INFO:root:cwltool --leave-tmpdir --outdir /mnt/c/@@@@@@@@TCF1_T_scATAC/new/ /root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/MICA/cwl/mica.cwl /mnt/c/@@@@@@@@TCF1_T_scATAC/new/mica.yml
INFO /root/miniconda3/envs/omicverse6/bin/cwltool 3.0.20210124104916
INFO Resolved '/root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/MICA/cwl/mica.cwl' to 'file:///root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/MICA/cwl/mica.cwl'
INFO [workflow ] start
INFO [workflow ] starting step prep
INFO [step prep] start
INFO [job prep] /tmp/yaoonq_5$ prep.py
-i
/tmp/29l_o7i3/stg1f004596-266a-4d71-b37b-9a6a03ba4e1f/CD8TMICA.h5ad
-o
TRAMP
-s
1000
ERROR Exception while running job
Traceback (most recent call last):
File "/root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/cwltool/job.py", line 388, in _execute
default_stderr=runtimeContext.default_stderr,
File "/root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/cwltool/job.py", line 948, in _job_popen
universal_newlines=True,
File "/root/miniconda3/envs/omicverse6/lib/python3.7/subprocess.py", line 800, in init
restore_signals, start_new_session)
File "/root/miniconda3/envs/omicverse6/lib/python3.7/subprocess.py", line 1551, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: 'prep.py'
WARNING [job prep] completed permanentFail
ERROR [step prep] Output is missing expected field file:///root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/MICA/cwl/mica.cwl#prep/mat_pair_array
WARNING [step prep] completed permanentFail
INFO [workflow ] completed permanentFail
{
"clustering_plots": null,
"clustering_res": null,
"initial_plots": null,
"mi.h5": null,
"mi.reduced": null
}
WARNING Final process status is permanentFail
Traceback (most recent call last):
File "/root/miniconda3/envs/omicverse6/bin/mica", line 33, in
sys.exit(load_entry_point('MICA==0.2.2', 'console_scripts', 'mica')())
File "/root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/MICA/mica.py", line 96, in main
mica_mds.mica_mds(args)
File "/root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/MICA/mica_mds.py", line 122, in mica_mds
run_shell_command_call(cmd)
File "/root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/MICA/mica_mds.py", line 162, in run_shell_command_call
subprocess.check_call(cmd_to_exec)
File "/root/miniconda3/envs/omicverse6/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cwltool', '--leave-tmpdir', '--outdir', '/mnt/c/@@@@@@@@TCF1_T_scATAC/new/', '/root/miniconda3/envs/omicverse6/lib/python3.7/site-packages/MICA/cwl/mica.cwl', '/mnt/c/@@@@@@@@TCF1_T_scATAC/new/mica.yml']' returned non-zero exit status 1.
(omicverse6) root@jiang:/home/jzhou/MICA/MICA/bin#

Can you help me?

best
Jiang

Hello! I am trying to run the tutorial of scMINER using the typical 10x format files (matrix, features or genes, barcodes) that are included in the MICA package (\MICA\test_data\inputs\10x\PBMC\3k\filtered_gene_bc_matrices\hg19) and everything runs smoothly until I get to the step:

Prepare MICA input

library(anndata)
generateMICAinput(eset = pbmc.14k.eset.log2, filepath = "./MICA_input.h5ad")

Next, when I am trying to process this file in MICA (Ubuntu, app in Windows) I am getting the following error:

(py376) geogav@ws-70-68:~/MICA$ mica ge -i ./test_data/inputs/10x/PBMC/3k/pre-processed/MICAexample.h5ad -o ./test_data/
outputs -nw 12
INFO:root:Start GE mode...
INFO:root:Read preprocessed expression matrix ...
Traceback (most recent call last):
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/site-packages/anndata/_io/utils.py", line 156, in func_wrapper
    return func(elem, *args, **kwargs)
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 532, in read_group
    EncodingVersions[encoding_type].check(
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/enum.py", line 352, in __getitem__
    return cls._member_map_[name]
KeyError: 'dict'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/geogav/anaconda3/envs/py376/bin/mica", line 8, in <module>
    sys.exit(main())
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/site-packages/MICA/mica.py", line 91, in main
    mica_ge.mica_ge(args)
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/site-packages/MICA/mica_ge.py", line 93, in mica_ge
    adata = pp.read_preprocessed_mat(args.input_file)
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/site-packages/MICA/lib/preprocessing.py", line 21, in read_preprocessed_mat
    adata = anndata.read_h5ad(in_file)
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/site-packages/anndata/_io/h5ad.py", line 426, in read_h5ad
    d[k] = read_attribute(f[k])
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/functools.py", line 840, in wrapper
    return dispatch(args[0].__class__)(*args, **kw)
  File "/home/geogav/anaconda3/envs/py376/lib/python3.7/site-packages/anndata/_io/utils.py", line 163, in func_wrapper
    f"Above error raised while reading key {elem.name!r} of "
anndata._io.utils.AnnDataReadError: Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Grou

Interestingly, MICA works smoothly with the toy dataset that MICA contains (pbmc3k_preprocessed.h5ad) (MICA\test_data\inputs\10x\PBMC\3k\pre-processed) and with several unprocessed .h5ad files.

I am quite buffled on what could be the problem with the scMINER pipeline so any help would be much appreciated!
:)