Example 3 producing blank results

[huynhvivian]

When following example 4.3 from the tutorial, I get blank files (other than the column and row names) for both the flux and balance files. What could be a reason for this?

[changwn]

The new version of tutorial was released. Can you paste your example here for debug? Thanks.

[huynhvivian]

I am running the following code with the newest version of scFEA (as of Jan 5):

python src/scFEA.py --data_dir data --input_dir input \
--test_file GSE72056_full.csv \
--moduleGene_file module_gene_iron_m15.csv \
--stoichiometry_matrix cmMat_iron_c8_m15.csv \
--cName_file cName_iron_c8_m15.csv \
--output_flux_file output/example3_flux_new.csv \
--output_balance_file output/example3_balance_new.csv

However, my output files are both blank:

$ head example3_flux_new.csv
,M_1,M_2,M_3,M_4,M_5,M_6,M_7,M_8,M_9,M_10,M_11,M_12,M_13,M_14,M_15
Cy72_CD45_H02_S758_comb,,,,,,,,,,,,,,,
CY58_1_CD45_B02_S974_comb,,,,,,,,,,,,,,,
Cy71_CD45_D08_S524_comb,,,,,,,,,,,,,,,
Cy81_FNA_CD45_B01_S301_comb,,,,,,,,,,,,,,,
Cy80_II_CD45_B07_S883_comb,,,,,,,,,,,,,,,
Cy81_Bulk_CD45_B10_S118_comb,,,,,,,,,,,,,,,
Cy72_CD45_D09_S717_comb,,,,,,,,,,,,,,,
Cy74_CD45_A03_S387_comb,,,,,,,,,,,,,,,
Cy71_CD45_B05_S497_comb,,,,,,,,,,,,,,,


$ head example3_balance_new.csv

,Fe2_ecm,Fe2_cyto,Fe3_lyso,Heme_phago,Fe2_mito,Heme_mito,OH,Fe3_cyto
Cy72_CD45_H02_S758_comb,,,,,,,,
CY58_1_CD45_B02_S974_comb,,,,,,,,
Cy71_CD45_D08_S524_comb,,,,,,,,
Cy81_FNA_CD45_B01_S301_comb,,,,,,,,
Cy80_II_CD45_B07_S883_comb,,,,,,,,
Cy81_Bulk_CD45_B10_S118_comb,,,,,,,,
Cy72_CD45_D09_S717_comb,,,,,,,,
Cy74_CD45_A03_S387_comb,,,,,,,,
Cy71_CD45_B05_S497_comb,,,,,,,,

[sukyorsuki]

same question. Have you ever solved this problem?

[sukyorsuki]

@huynhvivian

[niuruize]

Have you ever solved this problem?

[ZZZhuLF]

I also encountered this problem, someone can answer it?