empty output file

[zjgt]

Hi, I ran the test command, everything seems to be fine but the output file (consensus_networkncol.txt) is empty (76 bytes). What could be the possible reason? Also, what is the best way to export an expression matrix from R to be compatible with the input format? I always have to delete double quotes around the strings when using the write.table function.

(py374) me@MacBook-Pro-2 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: /Users/me/Documents/GitHub/tabula-muris-senis/Data/MACA/bulk_data/ARACNe-AP3/GSE_Gene_Folder/SJARACNe/test_data/inputs/BRCA100.exp probe_file: class: File path: /Users/me/Documents/GitHub/tabula-muris-senis/Data/MACA/bulk_data/ARACNe-AP3/GSE_Gene_Folder/SJARACNe/test_data/inputs/tf.txt p_value_consensus: 1e-05 p_value_bootstrap: 1e-07 depth: 40 aracne_config_dir: class: Directory path: /Users/me/opt/anaconda3/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 /Users/me/opt/anaconda3/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 /Users/me/opt/anaconda3/envs/py374/bin/cwltool 3.1.20220119140128 INFO Resolved '/Users/me/opt/anaconda3/envs/py374/lib/python3.7/site-packages/SJARACNe-0.2.1-py3.7.egg/SJARACNe/cwl/sjaracne_workflow.cwl' to 'file:///Users/me/opt/anaconda3/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 [step create_seeds] start INFO [workflow ] starting step ch_ending_exp INFO [step ch_ending_exp] start INFO [workflow ] start INFO [workflow ] starting step create_adjmat_names INFO [step create_adjmat_names] start INFO [workflow ] starting step validate_files INFO [step validate_files] start INFO [job ch_ending_exp] /private/tmp/docker_tmp7obqriib$ ch_line_ending.py \ -i \ BRCA100.exp INFO [workflow ] starting step ch_ending_probe INFO [step ch_ending_probe] start INFO [job validate_files] /private/tmp/docker_tmpfxaywulf$ QC_input.py \ -e \ BRCA100.exp \ -g \ tf.txt INFO [job ch_ending_probe] /private/tmp/docker_tmpcpcd_806$ 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 [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] /private/tmp/docker_tmpl81aw14o$ sjaracne.exe \ -i \ /private/tmp/docker_tmp15399vo4/stg55dafd91-44c8-4389-8df6-60ac7b1c80b7/BRCA100.exp \ -l \ /private/tmp/docker_tmp15399vo4/stg7948ea55-4804-403b-be2d-5fdaced8d6b3/tf.txt \ -s \ /private/tmp/docker_tmp15399vo4/stg7948ea55-4804-403b-be2d-5fdaced8d6b3/tf.txt \ -p \ 1e-07 \ -e \ 0 \ -a \ adaptive_partitioning \ -r \ 1 \ -H \ /private/tmp/docker_tmp15399vo4/stg0c62de08-8d48-4744-a70a-65a945e3a2d9/config \ -N \ 40 \ -o \ TF_run_001.adj \ -S \ 1 Displaying parameters

[PARA] Input file: /private/tmp/docker_tmp15399vo4/stg55dafd91-44c8-4389-8df6-60ac7b1c80b7/BRCA100.exp [PARA] Output file: TF_run_001.adj [PARA] MI P-value: 1e-07 [PARA] DPI tolerance: 0 INFO [job bootstrap_2] /private/tmp/docker_tmp5tw8iri3$ sjaracne.exe \ -i \ /private/tmp/docker_tmp66scs3v6/stgc6734db1-38c2-47ef-806c-3a703e249c46/BRCA100.exp \ -l \ /private/tmp/docker_tmp66scs3v6/stg01828072-9cdb-4d56-91fa-d5aeedf30ba4/tf.txt \ -s \ /private/tmp/docker_tmp66scs3v6/stg01828072-9cdb-4d56-91fa-d5aeedf30ba4/tf.txt \ -p \ 1e-07 \ -e \ 0 \ -a \ adaptive_partitioning \ -r \ 1 \ -H \ /private/tmp/docker_tmp66scs3v6/stg981983cd-7e89-4a77-adac-0bdc3a5e063a/config \ -N \ 40 \ -o \ TF_run_002.adj \ -S \ 2 [PARA] Subset of probes to reconstruct: /private/tmp/docker_tmp15399vo4/stg7948ea55-4804-403b-be2d-5fdaced8d6b3/tf.txt (2608) [PARA] TF annotation list: /private/tmp/docker_tmp15399vo4/stg7948ea55-4804-403b-be2d-5fdaced8d6b3/tf.txt (2608) [PARA] Npar limit: 40

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

[PARA] Input file: /private/tmp/docker_tmp66scs3v6/stgc6734db1-38c2-47ef-806c-3a703e249c46/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: /private/tmp/docker_tmp66scs3v6/stg01828072-9cdb-4d56-91fa-d5aeedf30ba4/tf.txt (2608) [PARA] TF annotation list: /private/tmp/docker_tmp66scs3v6/stg01828072-9cdb-4d56-91fa-d5aeedf30ba4/tf.txt (2608) [PARA] Npar limit: 40

[READ] 0 Description lines bypassed. [READ] P-value columns not found. 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 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: 98 10%, time: 104 20%, time: 191 20%, time: 206 30%, time: 289 30%, time: 312 40%, time: 386 40%, time: 417 50%, time: 484 50%, time: 522 60%, time: 584 60%, time: 629 70%, time: 683 70%, time: 737 80%, time: 780 80%, time: 841 90%, time: 876 90%, time: 947 Gene: 2608 Time: 975 [NETWORK] Applying DPI ... DPI running time is: 22 Writing matrix: TF_run_001.adj Maximum observed npar: 4 INFO [job bootstrap] Max memory used: 31MiB INFO [job bootstrap] completed success Gene: 2608 Time: 1056 [NETWORK] Applying DPI ... DPI running time is: 72 Writing matrix: TF_run_002.adj Maximum observed npar: 5 INFO [job bootstrap_2] Max memory used: 43MiB 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] /private/tmp/docker_tmpbwqqp6k8$ create_consensus_network.py \ -a \ /private/tmp/docker_tmps2hu55p1/stg0f32d3cf-d297-49fe-b902-1f2f5071aa95/SJARACNE_out.final \ -p \ 1e-05 \ -e \ /private/tmp/docker_tmps2hu55p1/stgfe88ced8-c78a-4980-849a-0ecc54fe65ec/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: 97MiB INFO [job consensus] completed success INFO [step consensus] completed success INFO [workflow ] completed success { "out_dir": { "location": "file:///Users/me/Documents/GitHub/tabula-muris-senis/Data/MACA/bulk_data/ARACNe-AP3/GSE_Gene_Folder/SJARACNe/test_data/outputs/cwl/cwltool/SJARACNE_out.final/consensus_networkncol.txt", "basename": "consensus_networkncol.txt", "class": "File", "checksum": "sha1$823c13f202337831dc1033bc8ced26948e01267a", "size": 76, "path": "/Users/me/Documents/GitHub/tabula-muris-senis/Data/MACA/bulk_data/ARACNe-AP3/GSE_Gene_Folder/SJARACNe/test_data/outputs/cwl/cwltool/SJARACNE_out.final/consensus_networkncol.txt" } } INFO Final process status is success INFO:root:All done.

[liu7923]

I had the same problem. Have you find a way to resolve it? Thanks!

[zjgt]

No, I have to use the original ARACNe. I’m new to the field 😓

Sent from my iPhone

On Jan 28, 2022, at 3:05 PM, liu7923 @.***> wrote:

 I had the same problem. Have you find a way to resolve it? Thanks!

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.

[adamdingliang]

For the empty output problem, it is most likely due to gene IDs in the TF or SIG list file do not match with the gene IDs in the input expression file. Also, make sure the format of your input expression matrix file is a tab-separated genes/protein by cells/samples expression matrix with the first two columns being ID and symbol, see test data https://github.com/jyyulab/SJARACNe/blob/master/test_data/inputs/BRCA100.exp for an example.

[adamdingliang]

Please reopen this issue if you still have this problem. Thanks.

[liu7923]

Thanks for your reply. I actually ran the example command provided in ReadMe file (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). It seems everything is good, but he output file (consensus_networkncol.txt) is empty. I double checked the gene IDs in input expression file (BRCA100.exp) and TF list file (tf.txt), and they matched very well. Please let me know if you have any other idea about this problem. Thank you very much!

[liu7923]

Thanks for your reply. I actually ran the example command provided in ReadMe file (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). It seems everything is good, but the output file (consensus_networkncol.txt) is empty. I double checked the gene IDs in the input expression file (BRCA100.exp) and TF list file (tf.txt), and they matched very well. Please let me know if you have any other ideas about this problem. Thank you very much!

Best regards, Lili

On Fri, Jan 28, 2022 at 7:55 PM Liang (Adam) Ding @.***> wrote:

Closed #36 https://github.com/jyyulab/SJARACNe/issues/36.

— Reply to this email directly, view it on GitHub https://github.com/jyyulab/SJARACNe/issues/36#event-5974214386, or unsubscribe https://github.com/notifications/unsubscribe-auth/AG7OD6DI2G6KSQISV757QHLUYM3H3ANCNFSM5MTRZAMA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you commented.Message ID: @.***>