pathview results blank on new run, but rerun works

usegalaxy.org support
1

Hi,
I am trying to run pathview and I am able to rerun an older successful run. But when I use the same files and parameters for a new run, the result is blank. The only difference I can see is the version of R being called. Any help would be appreciated.

This is from successful run:

Dataset Information
Number 644
Name Pathview on data 579: KEGG Pathway (hsa04110)
Created Thursday Apr 27th 18:01:23 2023 UTC
Filesize 39.2 KB
Dbkey ?
Format png
File contents contents

History Content API ID f9cad7b01a4721357dcb99120af50fb9
History API ID c021ab077c93c097
UUID 7fbec6b2-a1b8-4563-a6fc-25704eb457fd
Originally Created From a File Named *.pathview.png
Tool Parameters
Input Parameter Value
Number of pathways to plot one
KEGG pathway 04110
Species to use Human
Provide a gene data file? true
Gene data 579 : Pathview_input_GenesFC_A_AV.txt
Does the file have header (a first line with sample names)? True
Format for gene data Gene Symbol
Provide a compound data file? false
Should multiple states of gene or compond data be intergrated and plotted in the same graph? True
Are the gene and compound data paired? True
out
Output for pathway TRUE
Plot on same layer? True
Map the NULL gene or compound data to pathway? True

Job Outputs
Tool Outputs Dataset
Pathview on : KEGG Pathway (hsa04110) 644 : Pathview on data 579: KEGG Pathway (hsa04110)
Job Information
Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.24.0+galaxy0
Command Line empty
Tool Standard Output R version 3.6.2 (2019-12-12) Platform: x86_64-conda_cos6-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-2cf70d41d6f77f52fd82bcc11c23352d038782e2655597c8cc832856e04ad6a5/lib/libopenblasp-r0.3.7.so locale: [1] LC_CTYPE=C LC_NUMERIC=C LC_TIME=C [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] optparse_1.6.2 pathview_1.24.0 org.Hs.eg.db_3.8.2 [4] AnnotationDbi_1.46.0 IRanges_2.18.2 S4Vectors_0.22.0 [7] Biobase_2.44.0 BiocGenerics_0.30.0 loaded via a namespace (and not attached): [1] graph_1.62.0 Rcpp_1.0.3 KEGGgraph_1.44.0 XVector_0.24.0 [5] zlibbioc_1.30.0 getopt_1.20.3 bit_1.1-15.1 R6_2.4.1 [9] rlang_0.4.4 httr_1.4.1 blob_1.2.1 tools_3.6.2 [13] grid_3.6.2 png_0.1-7 DBI_1.1.0 bit64_0.9-7 [17] digest_0.6.23 Rgraphviz_2.28.0 vctrs_0.2.2 bitops_1.0-6 [21] KEGGREST_1.24.0 RCurl_1.98-1.1 memoise_1.1.0 RSQLite_2.1.5 [25] compiler_3.6.2 Biostrings_2.52.0 XML_3.99-0.3 pkgconfig_2.0.3 $pathway_id [1] “04110” $pathway_id_header [1] FALSE $species [1] “hsa” $gene_data [1] “/corral4/main/objects/4/f/c/dataset_4fc869e3-174b-424b-a5e4-6ad42aec415f.dat” $gd_header [1] TRUE $gene_idtype [1] “symbol” $cpd_header [1] FALSE $cpd_idtype [1] “kegg” $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] “bottomright” $help [1] FALSE [1] “Note: 28 of 1093 unique input IDs unmapped.” conda_activate.log hsa04110.pathview.png hsa04110.png hsa04110.xml
Tool Standard Error ‘select()’ returned 1:1 mapping between keys and columns Info: Downloading xml files for hsa04110, 1/1 pathways… Info: Downloading png files for hsa04110, 1/1 pathways… ‘select()’ returned 1:1 mapping between keys and columns Info: Working in directory /corral4/main/jobs/049/763/49763207/working Info: Writing image file hsa04110.pathview.png
Tool Exit Code: 0
Job API ID: bbd44e69cb8906b56e6a409f3fb4a818
Dataset Storage
This dataset is stored in a Galaxy object store with id corral4.
Inheritance Chain
Pathview on data 579: KEGG Pathway (hsa04110)
Job Metrics
cgroup
CPU Time 34.171355921 seconds
Failed to allocate memory count 0E-7
Memory limit on cgroup (MEM) 8.0 EB
Max memory usage (MEM) 595.3 MB
Memory limit on cgroup (MEM+SWP) 8.0 EB
Max memory usage (MEM+SWP) 595.3 MB
OOM Control enabled Yes
Was OOM Killer active? No
Memory softlimit on cgroup 8.0 EB
core
Cores Allocated 1
Memory Allocated (MB) 7680
Job Start Time 2023-04-27 13:01:26
Job End Time 2023-04-27 13:02:12
Job Runtime (Wall Clock) 46 seconds
cpuinfo
Processor Count 32
meminfo
Total System Memory 122.8 GB
Total System Swap 1000.0 MB
uname
Operating System Linux roundup64 3.10.0-1160.11.1.el7.x86_64 #1 SMP Fri Dec 18 16:34:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Dataset Peek
Image in png format

This is from run that produces zero bytes png:
Dataset Information
Number 642
Name Pathview on data 579: KEGG Pathway (hsa04110)
Created Thursday Apr 27th 17:57:53 2023 UTC
Filesize -
Dbkey ?
Format png
File contents contents

History Content API ID f9cad7b01a4721354f0e14f6ee64a5ac
History API ID c021ab077c93c097
UUID bc8fc980-90f5-4d08-9c5d-522d7558bd69
Originally Created From a File Named *.pathview.png
Tool Parameters
Input Parameter Value
Number of pathways to plot one
KEGG pathway 04110
Species to use Human
Provide a gene data file? true
Gene data 579 : Pathview_input_GenesFC_A_AV.txt
Does the file have header (a first line with sample names)? True
Format for gene data Gene Symbol
Provide a compound data file? false
Should multiple states of gene or compond data be intergrated and plotted in the same graph? True
Are the gene and compound data paired? True
out
Output for pathway TRUE
Plot on same layer? True
Map the NULL gene or compound data to pathway? True

Job Outputs
Tool Outputs Dataset
Pathview on : KEGG Pathway (hsa04110) 642 : Pathview on data 579: KEGG Pathway (hsa04110)
Job Information
Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.34.0+galaxy0
Command Line empty
Tool Standard Output R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.20.so locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] optparse_1.7.1 pathview_1.34.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 compiler_4.1.3 GenomeInfoDb_1.30.0 [4] XVector_0.34.0 bitops_1.0-7 tools_4.1.3 [7] zlibbioc_1.40.0 bit_4.0.4 RSQLite_2.2.8 [10] memoise_2.0.1 pkgconfig_2.0.3 png_0.1-7 [13] rlang_1.0.2 KEGGgraph_1.54.0 graph_1.72.0 [16] DBI_1.1.2 cli_3.3.0 Rgraphviz_2.38.0 [19] fastmap_1.1.0 GenomeInfoDbData_1.2.7 httr_1.4.3 [22] Biostrings_2.62.0 S4Vectors_0.32.3 vctrs_0.4.1 [25] IRanges_2.28.0 getopt_1.20.3 stats4_4.1.3 [28] bit64_4.0.5 grid_4.1.3 Biobase_2.54.0 [31] R6_2.5.1 AnnotationDbi_1.56.1 XML_3.99-0.9 [34] blob_1.2.3 org.Hs.eg.db_3.14.0 BiocGenerics_0.40.0 [37] KEGGREST_1.34.0 RCurl_1.98-1.6 cachem_1.0.6 [40] crayon_1.5.1 $pathway_id [1] “04110” $pathway_id_header [1] FALSE $species [1] “hsa” $gene_data [1] “/corral4/main/objects/4/f/c/dataset_4fc869e3-174b-424b-a5e4-6ad42aec415f.dat” $gd_header [1] TRUE $gene_idtype [1] “symbol” $cpd_header [1] FALSE $cpd_idtype [1] “kegg” $multi_state [1] TRUE $match_data [1] TRUE $kegg_native [1] TRUE $same_layer [1] TRUE $map_null [1] TRUE $split_group [1] FALSE $expand_node [1] FALSE $sign_pos [1] “bottomright” $help [1] FALSE [1] “Note: 1 of 1093 unique input IDs unmapped.”
Tool Standard Error Warning message: In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) : OS reports request to set locale to “en_US.UTF-8” cannot be honored ‘select()’ returned 1:1 mapping between keys and columns Info: Downloading xml files for hsa04110, 1/1 pathways… Warning: Download of hsa04110 xml file failed! This pathway may not exist! Info: Downloading png files for hsa04110, 1/1 pathways… Warning: Download of hsa04110 png file failed! This pathway may not exist! Warning: Failed to download KEGG xml/png files, hsa04110 skipped! Warning message: In download.file(xml.url, xml.target, quiet = T) : URL ‘https://rest.kegg.jp/get/hsa04110/kgml’: status was ‘Failure when receiving data from the peer’
Tool Exit Code: 0
Job API ID: bbd44e69cb8906b5c907b75dc27a13fe
Dataset Storage
This dataset is stored in a Galaxy object store with id corral4.
Inheritance Chain
Pathview on data 579: KEGG Pathway (hsa04110)
Job Metrics
cgroup
CPU Time 28.588011879 seconds
Failed to allocate memory count 0E-7
Memory limit on cgroup (MEM) 8.0 EB
Max memory usage (MEM) 461.2 MB
Memory limit on cgroup (MEM+SWP) 8.0 EB
Max memory usage (MEM+SWP) 461.2 MB
OOM Control enabled Yes
Was OOM Killer active? No
Memory softlimit on cgroup 8.0 EB
core
Cores Allocated 1
Memory Allocated (MB) 7680
Job Start Time 2023-04-27 12:57:58
Job End Time 2023-04-27 12:58:33
Job Runtime (Wall Clock) 35 seconds
cpuinfo
Processor Count 32
meminfo
Total System Memory 122.8 GB
Total System Swap 1000.0 MB
uname
Operating System Linux roundup61 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 7 15:41:52 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Dataset Peek
Image in png format

2

Hi @Lzprry

As a quick guess, the tool version is probably different between the runs, and one of them has a dependency issue, possibly on the specific cluster node where this tool ran or all nodes in that cluster, and maybe everywhere but that will need to checked.

Please try this:

  1. Rerun the failed run with the most current version of the tool
  2. Also rerun the prior successful run using the most current version of the tool

If one or both fails, these details you posted are helpful but not enough to troubleshoot a dependency issue. If you don’t want to post back the shared history link, would you please send in a bug report? Please include a link to this topic in the bug report comments so I can find it with a search. Just one is enough, I’ll be able to see the other success/failures in that same history.

Note: UseGalaxy.org (only) had an issue with one of our sub-server resources yesterday and earlier today but that is now fixed, which is why I’m suggesting one more rerun in general, and using the most current tool version for a raft of reasons (any older version of any tool could have a bug :beetle: that may only show up in corner cases).

That said, the issue may be with an external data source, this is the clue. But that may “go away” or repeat, and could be our fault. Your tests and report will help to sort that out.

Warning message: In download.file(xml.url, xml.target, quiet = T) : URL ‘https://rest.kegg.jp/get/hsa04110/kgml’: status was ‘Failure when receiving data from the peer’

I think you’ve seen this, but as a reference: Troubleshooting errors

3

Thank you for your reply. I’m a bit new to this, so here is how I tried to follow your instructions (my apologies in advance if I am not understanding everything):

I can use a failed run and switch versions to 1.24.0+galaxy0 and then it produces a figure. If I switch a successful run to 1.34.0+galaxy0 then the figure is 0 bytes. I don’t get any error, so I’m not sure how to report the bug.

Screen Shot 2023-05-02 at 10.03.56 AM
Screen Shot 2023-05-02 at 10.03.56 AM1370×276 30.4 KB

1 Like
4

Hi @Lzprry

Thanks for the followup. Yes, the tool has a bug. For some reason I though it was fixed already. I did just ask the developers for an update on the issue ticket below.

Issue ticket, includes the how-to for the workaround: Bug: Pathview Galaxy Version 1.34.0+galaxy0 · Issue #4901 · galaxyproject/tools-iuc · GitHub. What to do is what you noticed at UseGalaxy.org only for now: the older version works, the newer version doesn’t.

The newer version works at UseGalaxy.eu already. Please try there instead.