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VIB-PSB / ksrates

ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
https://ksrates.readthedocs.io
GNU General Public License v3.0
15 stars 9 forks source link

No output files #56

Open abcbot123 opened 6 months ago

abcbot123 commented 6 months ago

Hi, I'm using the ksrates docker image. I have an issue with not getting relevant output files. Here are the codes I have run,

/usr/local/bin/ksrates init config_oxalis.txt
/usr/local/bin/ksrates paralogs-ks config_oxalis.txt --n-threads 16
/usr/local/bin/ksrates orthologs-ks config_oxalis.txt oxalis populus --n-threads 16
/usr/local/bin/ksrates orthologs-ks config_oxalis.txt oxalis arabidopsis --n-threads 16
/usr/local/bin/ksrates orthologs-ks config_oxalis.txt oxalis vitis --n-threads 16
/usr/local/bin/ksrates orthologs-analysis config_oxalis.txt
/usr/local/bin/ksrates plot-orthologs config_oxalis.txt
/usr/local/bin/ksrates orthologs-adjustment config_oxalis.txt
/usr/local/bin/ksrates plot-paralogs config_oxalis.txt
/usr/local/bin/ksrates plot-tree config_oxalis.txt
/usr/local/bin/ksrates paralogs-analyses config_oxalis.txt

When I check the errors, this is what I found this error related to i-adhore step,

INFO    Done
INFO    ---
INFO    Running wgd colinearity Ks pipeline...
INFO    No colinearity anchor pair Ks data, will run wgd colinearity Ks analysis
INFO    Checking external software...
INFO    This is i-ADHoRe v3.0.
INFO    Creating i-ADHoRe tmp directory /var/lib/condor/execute/slot1/dir_774720/paralog_distributions/wgd_oxalis/oxalis.ks_anchors_tmp
INFO    Parsing GFF file
INFO    Writing gene lists for i-ADHoRe
INFO    Writing families file for i-ADHoRe
INFO    Writing i-ADHoRe configuration file
INFO    Running i-ADHoRe 3.0...
INFO    i-adhore /var/lib/condor/execute/slot1/dir_774720/paralog_distributions/wgd_oxalis/oxalis.ks_anchors_tmp/i-adhore.conf
ERROR   i-ADHoRe execution failed with return code: -6
ERROR   i-ADHoRe standard error output:
i-adhore: /i-adhore/src/Profile.cpp:95: void Profile::createNodes(const std::set<Link>&, const std::vector<GeneList*>&, std::vector<std::vector<Node*> >&, bool, bool) const: Assertion `geneX.isPairWith(geneY)' failed.
ERROR   Exiting.
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Here are the other errors and warnings I got,

INFO    Finished 1242/1243 gene family analyses...
INFO    Finished 1243/1243 gene family analyses...
INFO    Finished all gene family analyses
INFO    Analysis done
INFO    Making results data frame
INFO    Removing tmp directory
INFO    ---
INFO    Done
INFO    Fri Mar  8 16:10:48 2024
INFO    Done
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Computing ortholog distribution peaks with related error
INFO    Fri Mar  8 16:10:48 2024
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Loading parameters and input files
WARNING Ortholog peak database [ortholog_peak_db.tsv] not found or empty: a new one is now generated.
WARNING Ortholog Ks list database [ortholog_ks_list_db.tsv] not found or empty: a new one is now generated.
INFO    
INFO    Oxalis oulophora and Populus trichocarpa:
INFO    - Extracting ortholog Ks list
INFO    - Computing distribution peak through bootstrap (200 iterations)
INFO    - Adding peak to ortholog peak database
INFO    - Adding Ks list to ortholog Ks list database
INFO    
INFO    Oxalis oulophora and Vitis vinifera:
INFO    - Extracting ortholog Ks list
INFO    - Computing distribution peak through bootstrap (200 iterations)
INFO    - Adding peak to ortholog peak database
INFO    - Adding Ks list to ortholog Ks list database
INFO    
INFO    Populus trichocarpa and Vitis vinifera:
INFO    - Extracting ortholog Ks list
WARNING   Ortholog Ks TSV file not found [populus_vitis.ks.tsv]. Skipping peak estimate.
INFO    
INFO    Arabidopsis thaliana and Oxalis oulophora:
INFO    - Extracting ortholog Ks list
INFO    - Computing distribution peak through bootstrap (200 iterations)
INFO    - Adding peak to ortholog peak database
INFO    - Adding Ks list to ortholog Ks list database
INFO    
INFO    Arabidopsis thaliana and Populus trichocarpa:
INFO    - Extracting ortholog Ks list
WARNING   Ortholog Ks TSV file not found [arabidopsis_populus.ks.tsv]. Skipping peak estimate.
INFO    
INFO    Arabidopsis thaliana and Vitis vinifera:
INFO    - Extracting ortholog Ks list
WARNING   Ortholog Ks TSV file not found [arabidopsis_vitis.ks.tsv]. Skipping peak estimate.
INFO    
WARNING Number of failed peak computations: 3
WARNING 
INFO    All done
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Plotting ortholog distributions for all ortholog trios
INFO    Fri Mar  8 16:10:51 2024
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Loading parameters and input files
INFO    
INFO    Plotting ortholog Ks distributions for species pair [Oxalis oulophora - Populus trichocarpa]
WARNING - Skipping all outspecies: not enough ortholog data available (PDF figure not generated)
INFO    
INFO    Plotting ortholog Ks distributions for species pair [Oxalis oulophora - Vitis vinifera]
WARNING - Skipping all outspecies: not enough ortholog data available (PDF figure not generated)
WARNING 
WARNING The species pairs listed below are not (yet) available in the ortholog databases
WARNING The trios involving such species pairs have not been plotted
WARNING 
WARNING Species pairs not yet available in both Ks peak and Ks list ortholog databases:
WARNING   Arabidopsis thaliana - Populus trichocarpa
WARNING   Arabidopsis thaliana - Vitis vinifera
WARNING   Populus trichocarpa - Vitis vinifera
WARNING 
WARNING Please compute their ortholog Ks data and/or add the ortholog data to the databases,
WARNING then rerun this step.
INFO    
INFO    All done
INFO    - - - - - - - - - - - - - - - - - - - - - - 
INFO    Rate-adjustment of ortholog Ks distributions
INFO    Fri Mar  8 16:10:52 2024
INFO    - - - - - - - - - - - - - - - - - - - - - - 
INFO    Loading parameters and input files
INFO    
INFO    Performing rate-adjustment of each divergent pair by using one or more outgroups:
INFO     - Adjusting the peak for [Oxalis oulophora] and [Populus trichocarpa] with outspecies [Vitis vinifera]
WARNING Couldn't process trio [Oxalis oulophora, Populus trichocarpa, Vitis vinifera]:
WARNING  - [Populus trichocarpa_Vitis vinifera] not in ortholog peak database.
INFO     - Adjusting the peak for [Oxalis oulophora] and [Populus trichocarpa] with outspecies [Arabidopsis thaliana]
WARNING Couldn't process trio [Oxalis oulophora, Populus trichocarpa, Arabidopsis thaliana]:
WARNING  - [Arabidopsis thaliana_Populus trichocarpa] not in ortholog peak database.
INFO     - Adjusting the peak for [Oxalis oulophora] and [Vitis vinifera] with outspecies [Arabidopsis thaliana]
WARNING Couldn't process trio [Oxalis oulophora, Vitis vinifera, Arabidopsis thaliana]:
WARNING  - [Arabidopsis thaliana_Vitis vinifera] not in ortholog peak database.
INFO    Rate-adjustment results for each trio saved in TSV format [adjustment_table_oxalis_all.tsv]
INFO    
INFO    Rate-adjustment results as consensus values saved in TSV format [adjustment_table_oxalis.tsv]
INFO    
INFO    All done
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Generating mixed paralog and ortholog distributions
INFO    Fri Mar  8 16:10:53 2024
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Loading parameters and input files
ERROR   Anchor pair Ks TSV file not found at default position [paralog_distributions/wgd_oxalis/oxalis.ks_anchors.tsv].
ERROR   Exiting
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Generating PDF of input tree with branch length equal to Ks distances
INFO    Fri Mar  8 16:10:54 2024
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Loading parameters and input files
WARNING Rate-adjustment data not available yet: PDF figure of phylogenetic tree not generated.
INFO    Exiting
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Clustering anchorpoints Ks values to reconstruct recent WGD events
INFO    Fri Mar  8 16:10:55 2024
INFO    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
INFO    Loading parameters and input files
INFO     - maximum EM iterations: 600
INFO     - number of EM initializations: 10
ERROR   anchorpoints.txt file not found at default position [paralog_distributions/wgd_oxalis/oxalis_i-adhore/anchorpoints.txt].
ERROR   multiplicons.txt file not found at default position [paralog_distributions/wgd_oxalis/oxalis_i-adhore/anchorpoints.txt].
ERROR   segments.txt file not found at default position [paralog_distributions/wgd_oxalis/oxalis_i-adhore/segments.txt].
ERROR   multiplicon_pairs.txt file not found at default position [paralog_distributions/wgd_oxalis/oxalis_i-adhore/multiplicon_pairs.txt].
ERROR   list_elements.txt file not found at default position [paralog_distributions/wgd_oxalis/oxalis_i-adhore/list_elements.txt].
ERROR   oxalis.ks_anchors.tsv file not found at default position [paralog_distributions/wgd_oxalis/oxalis.ks_anchors.tsv].
ERROR   Exiting

Do you have any suggestions to fix this error? Thanks so much!

Cecilia-Sensalari commented 6 months ago

Hi abcbot123 :)

Thanks for reaching out. At a first glance, the problem originates within i-ADHoRe, while the other warnings in the later commands arise from the fact that some orthologs Ks data are still not generated (probably interrupted by the error?).

The i-ADHoRe error message says:

ERROR i-ADHoRe execution failed with return code: -6
ERROR i-ADHoRe standard error output:
i-adhore: /i-adhore/src/Profile.cpp:95: void Profile::createNodes(const std::set&, 
const std::vector<GeneList*>&, std::vector<std::vector<Node*> >&, bool, bool) 
const: Assertion `geneX.isPairWith(geneY)' failed.

It's thus related to line 95 in file Profile.cpp. I never encountered such error and right now I don't know what can be causing it.

It seems to me that i-ADHoRe is not finding the data it expects to find. Could you double check if your GFF file follows the standard format and could you make sure you're parsing it with the correct gff_feature and gff_attribute? If you have successfully run other species in the past, can you think about something different in the input files?

Cheers, Cecilia

Cecilia-Sensalari commented 6 months ago

Here's an update :) I noticed that your error message is the same reported in a recent issue on i-ADHoRe itself. When building the ksrates docker container, we are actually basing it on the vib/i-adhore GitHub repo (see first line in our dockerfile). This makes me think that your issue is inherited from i-ADHoRe. I'll get in touch with its maintainers to look into that!

If the above is correct, then you should still be able to run ksrates using the whole-paranome pipeline, deactivating the colinearity pipeline (see configuration).

Best, Cecilia

Cecilia-Sensalari commented 6 months ago

Hi :) It would also probably still be helpful if you could provide us with your input FASTA and GFF files for Oxalis, as well as with the parsing gff_features and gff_attribute you have chosen. Thanks!

abcbot123 commented 5 months ago

Hi Cecilia, Thanks so much for your response. I have recheck my gff3 file and there was an issue with the format. I have fixed it and got the output files. But I'm struggling with how to explain my results. Could you please help me to figure out how to explain my output files? If so, I can send those .pdf files I got. Thanks so much!

Cecilia-Sensalari commented 5 months ago

Hi, I'm happy it was just a format issue! Feel free to share what it was if you think other people might encounter the same problem. Sure, we can have a look together at your output files. What about using gitter to communicate? You can sign in with your GitHub account, then we can share files and text. Cheers, Cecilia

abcbot123 commented 5 months ago

Hi Cecilia, Yes, I can do that. I have login to gitter using my GitHub account but I couldn't find you to sent a message.

wjq1981 commented 1 month ago

Hi, I'm having a similar problem, here's the code to run and the errors reported, can you help me see how to fix it?

ksrates plot-paralogs config_Bchinensis.txt

INFO Generating mixed paralog and ortholog distributions INFO Sun Jul 21 15:14:52 2024 INFO Loading parameters and input files ERROR Anchor pair Ks TSV file not found at default position [paralog_distributions/wgd_Bchinensis/Bchinensis.ks_anchors.tsv]. ERROR Exiting

# There is also an error in the above step

ksrates orthologs-analysis config_Bchinensis.txt

INFO Computing ortholog distribution peaks with related error INFO Sun Jul 21 15:31:43 2024

INFO Loading parameters and input files INFO INFO Belamcanda chinensis and Crocus sativus: data already present in ortholog database INFO INFO Asparagus officinal and Belamcanda chinensis: data already present in ortholog database INFO INFO Asparagus officinal and Crocus sativus: data already present in ortholog database INFO INFO All done

Cecilia-Sensalari commented 1 month ago

Hi wjq1981,

Thanks for reaching out!

The error originating from command plot-paralogs says that, while trying to plot the anchor pair Ks distribution, it doesn't find the file listing all the anchor pair Ks values; it also says that this file is normally located at paralog_distributions/wgd_Bchinensis/Bchinensis.ks_anchors.tsv. Have you already generated such file? To do so, you have to run command paralogs-ks also for the anchor pairs by setting collinearity = yes in configuration file config_Bchinensis.txt. If you did already generate it, have you perhaps moved it or renamed it? In that case, it doesn't find it. Or, perhaps you're lunching the command line from a wrong location, from which it can't find the file according to the default path.

The output from command orthologs-analysis doesn't have any error message :) The INFO lines say that the ortholog Ks distributions for all species pairs have been already generated and are already available in the ortholog database, so they are not calculated again.

Let me know how it goes, and if this doesn't help we can investigate further! Cheers, Cecilia

wjq1981 commented 1 month ago

Thank you for your prompt reply. 'collinearity = yes' is so in the “config_Bchinensis.txt” file. At the same time I didn't find the file “Bchinensis.ks_anchors.tsv” in any of the generated directories. And to rule out the possibility that it's just me, I ran “config_elaeis.txt” from test and got the same error!

ksrates plot-paralogs config_elaeis.txt INFO - - - - - - - - - - - - - - - - - - - - - - - - - - INFO Generating mixed paralog and ortholog distributions INFO Mon Jul 22 16:21:45 2024 INFO - - - - - - - - - - - - - - - - - - - - - - - - - - INFO Loading parameters and input files ERROR Anchor pair Ks TSV file not found at default position [paralog_distributions/wgd_elaeis/elaeis.ks_anchors.tsv]. ERROR Exiting

wjq1981 commented 1 month ago

This is a list of all the files in the “paralog_distributions” directory.

paralog_distributions/wgd_elaeis ├── elaeis.blast.tsv ├── elaeis.ks_anchors_tmp │   ├── families.tsv │   ├── i-adhore.conf │   ├── i-adhore_gene_lists │   │   ├── EG5.1_Chr10.lst │   │   ├── EG5.1_Chr11.lst │   │   ├── EG5.1_Chr12.lst │   │   ├── EG5.1_Chr13.lst │   │   ├── EG5.1_Chr14.lst │   │   ├── EG5.1_Chr15.lst │   │   ├── EG5.1_Chr16.lst │   │   ├── EG5.1_Chr1.lst │   │   ├── EG5.1_Chr2.lst │   │   ├── EG5.1_Chr3.lst │   │   ├── EG5.1_Chr4.lst │   │   ├── EG5.1_Chr5.lst │   │   ├── EG5.1_Chr6.lst │   │   ├── EG5.1_Chr7.lst │   │   ├── EG5.1_Chr8.lst │   │   ├── EG5.1_Chr9.lst │   │   ├── p5_sc00010.lst │   │   ├── .............. │   │   └── p5_sc40286.lst │   └── i-adhore_out │   ├── AlignmentMultiplicon1.svg │   ├── AlignmentMultiplicon2.svg │   ├── AlignmentMultiplicon3.svg │   ├── AlignmentMultiplicon4.svg │   ├── AlignmentMultiplicon5.svg │   ├── alignment.txt │   ├── anchorpoints.txt │   ├── baseclusters.txt │   ├── genes.txt │   ├── list_elements.txt │   ├── multiplicon_pairs.txt │   ├── multiplicons.txt │   └── segments.txt ├── elaeis.ks.tsv └── elaeis.mcl.tsv

Wouldn't 'elaeis.ks.tsv' be 'elaeis.ks_anchors.tsv' here either? Because it's the first time I've run it and I don't know what their contents should be!

Cecilia-Sensalari commented 1 month ago

Alright! In the docs you can find the description of the output files: for example here it explains that elaeis.ks.tsv and elaeis.ks_anchors.tsv are similar in content, but the first is the list of Ks values for all paralogs (paranome), while the second is restricted to only anchor pairs.

The directory structure can tell us something: normally elaeis.ks_anchors_tmp is a temporary directory that is deleted once the final elaeis.ks_anchors.tsv is obtained. Therefore, I think that command paralogs-ks encountered an error during its execution while computing anchor pairs; could you check its output log?

wjq1981 commented 1 month ago

This is the output log. # ksrates paralogs-ks config_elaeis.txt --n-threads=64

INFO - - - - - - - - - - - - - - - - - - - - - INFO Paralog wgd analysis for species [elaeis] INFO Mon Jul 22 16:57:41 2024 INFO - - - - - - - - - - - - - - - - - - - - - INFO Checking if sequence data files exist and if sequence IDs are compatible with wgd pipeline... INFO Completed INFO Creating directory [paralog_distributions/] INFO Running wgd paralog Ks pipeline... INFO --- INFO Checking external software... INFO makeblastdb: 2.5.0+ INFO blastp: 2.5.0+ INFO mcl 14-137 INFO MUSCLE v3.8.1551 by Robert C. Edgar INFO AAML in paml version 4.10.7, June 2023 INFO Usage for FastTree version 2.1.8 Double precision (No SSE3): INFO Creating output directory /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis INFO Translating CDS file elaeis.fasta... INFO --- INFO Running all versus all Blastp INFO Writing protein Blastdb sequences to /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.blast_tmp/... INFO Writing protein query sequences to /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.blast_tmp/... INFO Performing all versus all Blastp (this might take a while)... INFO Making Blastdb INFO makeblastdb -in /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.blast_tmp/elaeis.db.fasta -dbtype prot INFO makeblastdb output: Building a new DB, current time: 07/22/2024 16:57:42 New DB name: /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.blast_tmp/elaeis.db.fasta New DB title: /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.blast_tmp/elaeis.db.fasta Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 500 sequences in 0.108267 seconds. INFO Running Blastp INFO blastp -db /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.blast_tmp/elaeis.db.fasta -query /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.blast_tmp/elaeis.query.fasta -evalue 1e-10 -outfmt 6 -num_threads 64 -out /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.blast.tsv INFO All versus all Blastp done INFO Removing tmp directory INFO --- INFO Running gene family construction (MCL clustering with inflation factor = 2.0) INFO Started MCL clustering (mcl) INFO --- INFO Running whole paranome Ks analysis... INFO Started analysis of 66 gene families in parallel using 64 threads INFO Performing analysis on gene family GF_000001 (size 13) INFO Performing analysis on gene family GF_XXXXXX (size 2) INFO Performing analysis on gene family GF_000066 (size 2) INFO Finished 2/66 gene family analyses... INFO Finished 47/66 gene family analyses... INFO Finished 63/66 gene family analyses... INFO Finished 64/66 gene family analyses... INFO Finished 65/66 gene family analyses... INFO Finished 66/66 gene family analyses... INFO Finished all gene family analyses INFO Analysis done INFO Making results data frame INFO Computing weights, outlier cut-off at Ks > 20 INFO Removing tmp directory INFO --- INFO Done INFO --- INFO Running wgd colinearity Ks pipeline... INFO No colinearity anchor pair Ks data, will run wgd colinearity Ks analysis INFO Checking external software... INFO This is i-ADHoRe v3.0. INFO Creating i-ADHoRe tmp directory /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.ks_anchors_tmp INFO Parsing GFF file INFO Writing gene lists for i-ADHoRe INFO Writing families file for i-ADHoRe INFO Writing i-ADHoRe configuration file INFO Running i-ADHoRe 3.0... INFO i-adhore /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.ks_anchors_tmp/i-adhore.conf INFO i-ADHoRe output: This is i-ADHoRe v3.0. Copyright (c) 2002-2010, Flanders Interuniversity Institute for Biotechnology, VIB. Algorithm designed by Klaas Vandepoele, Cedric Simillion, Jan Fostier, Dieter De Witte, Koen Janssens, Sebastian Proost, Yvan Saeys and Yves Van de Peer.

Process 1/1 is alive on suma-Nd.

i-ADHoRe parameters Number of genelists = 2643 Blast table = /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.ks_anchors_tmp/families.tsv Output path = /dev/hdd/soft/ksrates/test/paralog_distributions/wgd_elaeis/elaeis.ks_anchors_tmp/i-adhore_out/ Gap size = 30 Cluster gap size = 35 Cloud gap size = 0 Cloud cluster gap size = 0 Max gaps in alignment = 35 Tandem gap = 15 Flush output = 1000 Q-value = 0.75 Anchorpoints = 3 Probability cutoff = 0.01 Cloud filtering method = Binomial Level 2 only = false Use family = true Write statistics = false Alignment method = GreedyGraphbased4 Multiple hypothesis correction = FDR Number of threads = 64 Compare aligners = false Collinear searches only Visualize GHM.png = false Visualize Alignment = true Verbose output = true **** END i-AdDHoRe parameters *****

Creating dataset... done. (time: 0.132908s) Mapping gene families... done. (time: 0.0924711s) Remapping tandem duplicates... done. (time: 0.043623s) Writing genelists file... done. (time: 0.480689s) Collinear Search Level 2 multiplicon detection... done. (time: 1.85592s) Profile detection... 5 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 4 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 3 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 2 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 1 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant Flushing output files...Visualize AlignedProfiles done. Time for Higher Level Detection: 0.075561s.

All Done! Bye... ERROR i-ADHoRe execution failed with standard error output: Authorization required, but no authorization protocol specified Authorization required, but no authorization protocol specified Authorization required, but no authorization protocol specified ERROR Exiting.

Cecilia-Sensalari commented 1 month ago

Based on the output log, i-ADHoRe was doing alright until the very end: it printed "All Done! Bye..." and then something generated an error with message "Authorization required, but no authorization protocol specified". I've never encountered this error and I don't know what it refers to. After a quick search online and a question to ChatGPT, I see that it is related to "Unix-like system using the X Window System (X11)", so to your environment where you are running ksrates/i-ADHoRe. I suggest you search this error and see whether some other users already had similar problems, or that you ask ChatGPT and/or your IT group for help. I'll have a look myself as well in the meantime, because I don't fully grasp the topic...

For example, here the problem was that the user was running commands as "root" and not as "user": https://www.reddit.com/r/linux4noobs/comments/lu1plx/hi_i_get_this_authorization_required_but_no/ and https://stackoverflow.com/questions/48833451/no-protocol-specified-when-running-a-sudo-su-app-on-ubuntu-linux

wjq1981 commented 1 month ago

Thank you very much for your answer. Another problem I have is that I'm getting errors running with docker, I uninstalled and reinstalled it and still get the same error, can you see if it's a software problem or a docker problem? I'm using other docker software and it's working.

docker run --rm -v $PWD:/temp -w /temp vibpsb/ksrates -h docker: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "-h": executable file not found in $PATH: unknown.

Cecilia-Sensalari commented 1 month ago

Let's see, here in the docs I showed how to use the docker commands, and it looks like you chose the one to "launch a single command through the container":

image

In order to run such command, for example -h, you need to typeksrates -h (and not only -h) at the end of the docker command line (compare with the command line in your previous message). Can you try again with the following edit? docker run --rm -v $PWD:/temp -w /temp vibpsb/ksrates ksrates -h Hope this helps!

wjq1981 commented 1 month ago

Yeah, you're right. Now that it's working with “ksrates”, I'm crying at my own stupidity. Good day！

Cecilia-Sensalari commented 1 month ago

No worries, great to hear this worked! Should you find an answer for the authorization-related error, let me know :)