# pathview results blank on new run, but rerun works **URL:** \ **Category:** usegalaxy.org support\ **Tags:** visualization, exceeds-memory-error\ **Created:** [April 27, 2023, 6:23pm UTC](https://help.galaxyproject.org/t/pathview-results-blank-on-new-run-but-rerun-works/9971 "2023-04-27T18:23:19Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Lzprry](https://avatars.discourse-cdn.com/v4/letter/l/ba8739/32.png) [@Lzprry](https://help.galaxyproject.org/u/Lzprry)\ **Post date:** [April 27, 2023, 6:23pm UTC](https://help.galaxyproject.org/t/pathview-results-blank-on-new-run-but-rerun-works/9971/1 "2023-04-27T18:23:19Z")
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](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 ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [April 27, 2023, 10:50pm UTC](https://help.galaxyproject.org/t/pathview-results-blank-on-new-run-but-rerun-works/9971/2 "2023-04-27T22:50:19Z")
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](http://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 🪲 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’:](https://rest.kegg.jp/get/hsa04110/kgml%E2%80%99:) status was ‘Failure when receiving data from the peer’ I think you’ve seen this, but as a reference: [Troubleshooting errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html) ---
**Author:** ![Lzprry](https://avatars.discourse-cdn.com/v4/letter/l/ba8739/32.png) [@Lzprry](https://help.galaxyproject.org/u/Lzprry)\ **Post date:** [May 2, 2023, 2:40pm UTC](https://help.galaxyproject.org/t/pathview-results-blank-on-new-run-but-rerun-works/9971/3 "2023-05-02T14:40:15Z")
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](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/3c9b6ab80f330367255a41c4b206abd3d71a321a.png) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [May 2, 2023, 4:48pm UTC](https://help.galaxyproject.org/t/pathview-results-blank-on-new-run-but-rerun-works/9971/4 "2023-05-02T16:48:21Z")
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](https://github.com/galaxyproject/tools-iuc/issues/4901). What to do is what you noticed at [UseGalaxy.org](http://UseGalaxy.org) only for now: the older version works, the newer version doesn’t. The newer version works at [UseGalaxy.eu](http://UseGalaxy.eu) already. Please try there instead. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [May 8, 2026, 2:03am UTC](https://help.galaxyproject.org/t/pathview-results-blank-on-new-run-but-rerun-works/9971/5 "2026-05-08T02:03:05Z")