empty output file about sjaracne

[jonathan-f]

Hello, I have exactly the same issue.

I have installed a conda environment with python 3.7.4 as suggested with the required packages and I am using SJARACNe version 0.2.1 on a machine with Ubuntu 18.04.5.

Any help would be appreciated.

Thanks
Best
Jonathan

[garciaaxnih]

Hi,

I am facing the same issue using the example command as well. Has there been any fix?

Thanks!

[msc245]

Hi,

I am facing the same issue using the example command as well. Has there been any fix?

Thanks!

[saisaitian]

(py374) tss1@bio-PowerEdge-T640:~/SJARACNe$ sjaracne local -e ./test_data/inputs/BRCA100.exp -g ./test_data/inputs/tf.txt -n 2 -o ./test_data/outputs/cwl/cwltool/SJARACNE_out.final
INFO:root:test_data/outputs/cwl/cwltool/SJARACNE_out.final/sjaracne_workflow.yml
INFO:root:exp_file:
  class: File
  path: /home/data/tss1/SJARACNe/test_data/inputs/BRCA100.exp
probe_file:
  class: File
  path: /home/data/tss1/SJARACNe/test_data/inputs/tf.txt
p_value_consensus: 1e-05
p_value_bootstrap: 1e-07
depth: 40
aracne_config_dir:
  class: Directory
  path: /home/data/tss1/miniconda3/envs/py374/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/config
bootstrap_num: 2
final_out_dir_name: SJARACNE_out.final
INFO:root:cwltool --parallel --outdir ./test_data/outputs/cwl/cwltool/SJARACNE_out.final /home/data/tss1/miniconda3/envs/py374/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl test_data/outputs/cwl/cwltool/SJARACNE_out.final/sjaracne_workflow.yml
INFO /home/data/tss1/miniconda3/envs/py374/bin/cwltool 3.1.20220628170238
INFO Resolved '/home/data/tss1/miniconda3/envs/py374/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl' to 'file:///home/data/tss1/miniconda3/envs/py374/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl'
INFO [workflow ] starting step create_seeds
INFO [workflow ] start
INFO [step create_seeds] start
INFO [workflow ] starting step ch_ending_exp
INFO [step ch_ending_exp] start
INFO [workflow ] starting step validate_files
INFO [step validate_files] start
INFO [job ch_ending_exp] /tmp/0e_sr7bh$ ch_line_ending.py \
    -i \
    BRCA100.exp
INFO [workflow ] starting step create_adjmat_names
INFO [step create_adjmat_names] start
INFO [workflow ] starting step ch_ending_probe
INFO [step ch_ending_probe] start
INFO [job validate_files] /tmp/kmyzrqw2$ QC_input.py \
    -e \
    BRCA100.exp \
    -g \
    tf.txt
INFO [job ch_ending_probe] /tmp/oipyo3d8$ ch_line_ending.py \
    -i \
    tf.txt
Unix line ending. No need to convert
Unix line ending. No need to convert
INFO [step create_seeds] completed success
INFO [step create_adjmat_names] completed success
INFO:root:Number of genes in expression matrix: 28278
INFO:root:Number of hub genes in probe file: 2608
INFO [job validate_files] completed success
INFO [step validate_files] completed success
INFO [job ch_ending_probe] completed success
INFO [step ch_ending_probe] completed success
INFO [job ch_ending_exp] completed success
INFO [step ch_ending_exp] completed success
INFO [workflow ] starting step bootstrap
INFO [step bootstrap] start
INFO [step bootstrap] start
INFO [job bootstrap] /tmp/qf8jjsob$ sjaracne.exe \
    -i \
    /tmp/iir2p7yd/stg66198979-8e36-4f70-980f-938606ad3f9a/BRCA100.exp \
    -l \
    /tmp/iir2p7yd/stga64eaf23-7b38-43a0-afbf-b95e9470b280/tf.txt \
    -s \
    /tmp/iir2p7yd/stga64eaf23-7b38-43a0-afbf-b95e9470b280/tf.txt \
    -p \
    1e-07 \
    -e \
    0 \
    -a \
    adaptive_partitioning \
    -r \
    1 \
    -H \
    /tmp/iir2p7yd/stg5eb30709-f4f8-48a5-b1f7-c4b9babd3122/config \
    -N \
    40 \
    -o \
    TF_run_001.adj \
    -S \
    1
INFO [job bootstrap_2] /tmp/lv_msu1l$ sjaracne.exe \
    -i \
    /tmp/cw7agx5q/stgcaa94e5a-9067-4605-85ff-117c848bdaa5/BRCA100.exp \
    -l \
    /tmp/cw7agx5q/stgf0e92bbc-7a85-4fbf-8cfe-83b7b053cb11/tf.txt \
    -s \
    /tmp/cw7agx5q/stgf0e92bbc-7a85-4fbf-8cfe-83b7b053cb11/tf.txt \
    -p \
    1e-07 \
    -e \
    0 \
    -a \
    adaptive_partitioning \
    -r \
    1 \
    -H \
    /tmp/cw7agx5q/stgfc66403d-66eb-4ce4-a2d7-2b7aac8a701e/config \
    -N \
    40 \
    -o \
    TF_run_002.adj \
    -S \
    2
Displaying parameters

[PARA] Input file:    /tmp/iir2p7yd/stg66198979-8e36-4f70-980f-938606ad3f9a/BRCA100.exp
[PARA] Output file:   TF_run_001.adj
[PARA] MI P-value:    1e-07
[PARA] DPI tolerance: 0
[PARA] Subset of probes to reconstruct: /tmp/iir2p7yd/stga64eaf23-7b38-43a0-afbf-b95e9470b280/tf.txt (2608)
[PARA] TF annotation list: /tmp/iir2p7yd/stga64eaf23-7b38-43a0-afbf-b95e9470b280/tf.txt (2608)
[PARA] Npar limit:    40

[READ] 0 Description lines bypassed.
[READ] P-value columns not found.
Displaying parameters

[PARA] Input file:    /tmp/cw7agx5q/stgcaa94e5a-9067-4605-85ff-117c848bdaa5/BRCA100.exp
[PARA] Output file:   TF_run_002.adj
[PARA] MI P-value:    1e-07
[PARA] DPI tolerance: 0
[PARA] Subset of probes to reconstruct: /tmp/cw7agx5q/stgf0e92bbc-7a85-4fbf-8cfe-83b7b053cb11/tf.txt (2608)
[PARA] TF annotation list: /tmp/cw7agx5q/stgf0e92bbc-7a85-4fbf-8cfe-83b7b053cb11/tf.txt (2608)
[PARA] Npar limit:    40

[READ] 0 Description lines bypassed.
[READ] P-value columns not found.
Marker No: 28278 (28278 active), Array No: 100
MI threshold determined for p=1e-07: 0.153257
Marker No: 28278 (28278 active), Array No: 100
MI threshold determined for p=1e-07: 0.153257
10%, time: 82
10%, time: 84
20%, time: 166
20%, time: 166
30%, time: 247
30%, time: 248
40%, time: 331
40%, time: 332
50%, time: 416
50%, time: 418
60%, time: 495
60%, time: 497
70%, time: 576
70%, time: 578
80%, time: 658
80%, time: 661
90%, time: 740
90%, time: 742
Gene: 2608 Time: 821
[NETWORK] Applying DPI ...
Gene: 2608 Time: 823
[NETWORK] Applying DPI ...
DPI running time is: 46
Writing matrix: TF_run_001.adj
Maximum observed npar: 4
INFO [job bootstrap] Max memory used: 54MiB
INFO [job bootstrap] completed success
DPI running time is: 79
Writing matrix: TF_run_002.adj
Maximum observed npar: 4
INFO [job bootstrap_2] Max memory used: 55MiB
INFO [job bootstrap_2] completed success
INFO [step bootstrap] completed success
INFO [workflow ] starting step copy_to_dir
INFO [step copy_to_dir] start
INFO [step copy_to_dir] completed success
INFO [workflow ] starting step consensus
INFO [step consensus] start
INFO [job consensus] /tmp/dbtk7o0i$ create_consensus_network.py \
    -a \
    /tmp/7ww6dysz/stg20fe3d99-ccf9-49f1-955d-0d27a93baf70/SJARACNE_out.final \
    -p \
    1e-05 \
    -e \
    /tmp/7ww6dysz/stgc3268edc-efad-45da-8ead-06c98be5326b/BRCA100.exp \
    -o \
    SJARACNE_out.final
INFO:root:Create an initial consensus network ...
INFO:root:Done
INFO:root:Create an enhanced consensus network ...
INFO:root:All done
INFO [job consensus] Max memory used: 192MiB
INFO [job consensus] completed success
INFO [step consensus] completed success
INFO [workflow ] completed success
{
    "out_dir": {
        "location": "file:///home/data/tss1/SJARACNe/test_data/outputs/cwl/cwltool/SJARACNE_out.final/consensus_network_ncol_.txt",
        "basename": "consensus_network_ncol_.txt",
        "class": "File",
        "checksum": "sha1$823c13f202337831dc1033bc8ced26948e01267a",
        "size": 76,
        "path": "/home/data/tss1/SJARACNe/test_data/outputs/cwl/cwltool/SJARACNE_out.final/consensus_network_ncol_.txt"
    }
}
INFO Final process status is success
INFO:root:All done.

everything is ok，but the output is empty! could you tell me how to solve it?

[adamdingliang]

See issue #39.