java.net.UnknownHostException: gseaftp.broadinstitute.org

[Lauro Sumoy Van Dyck]

Dear GSEA teams contact person,

I have been running several series of gsea-cli.sh executions from linux without issues but just encountered repeated failed runs with the following error:

java.net.UnknownHostException: gseaftp.broadinstitute.org

...

is it possible that there is some network or DNS filtering going on?

Example of command line:

/home/labs/lslab/lsumoy/GSEA_Linux_4.3.3/gsea-cli.sh GSEAPreranked -gmx /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_input/keratinocyte.genesets.v2026.1.Hs.gmt -collapse Collapse -mode Max_probe -norm meandiv -nperm 1000 -rnk /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/cmp01_C4_vs_C0_prom_diffmeth_difB_entrez.rnk -scoring_scheme weighted -rpt_label keratinocyte._cmp01_C4_vs_C0_difB_ -chip /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/Human_NCBI_Entrez_Gene_ID_MSigDB.v7.2.chip -create_svgs false -include_only_symbols true -make_sets true -plot_top_x 20 -rnd_seed 149 -set_max 500 -set_min 15 -zip_report false -out /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_output

output screen log:

echo Using bundled JDK.
WARNING: package com.apple.laf not in java.desktop
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
[1771935663052] [INFO] Parameters passing to GSEAPreranked.main:
[1771935663111] [INFO] rnk /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/cmp01_C4_vs_C0_prom_diffmeth_difB_entrez.rnk
[1771935663111] [INFO] gmx /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_input/keratinocyte.genesets.v2026.1.Hs.gmt
[1771935663112] [INFO] rnd_seed 149
[1771935663112] [INFO] rpt_label keratinocyte._cmp01_C4_vs_C0_difB_
[1771935663112] [INFO] collapse Collapse
[1771935663112] [INFO] zip_report false
[1771935663113] [INFO] gui false
[1771935663113] [INFO] out /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_output
[1771935663113] [INFO] chip /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/Human_NCBI_Entrez_Gene_ID_MSigDB.v7.2.chip
[1771935663114] [INFO] mode Max_probe
[1771935663114] [INFO] norm meandiv
[1771935663114] [INFO] nperm 1000
[1771935663115] [INFO] scoring_scheme weighted
[1771935663115] [INFO] include_only_symbols true
[1771935663115] [INFO] make_sets true
[1771935663116] [INFO] plot_top_x 20
[1771935663116] [INFO] rnd_seed 149
[1771935663116] [INFO] create_svgs false
[1771935663116] [INFO] set_max 500
[1771935663117] [INFO] set_min 15
[1771935663174] [INFO] Begun importing: RankedList from: /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/cmp01_C4_vs_C0_prom_diffmeth_difB_entrez.rnk
[1771935664509] [WARNING] Duplicate GeneSet member: 79166
[1771935664511] [WARNING] Duplicate GeneSet member: 445347
[1771935664511] [WARNING] Duplicate GeneSet member: 5664
[1771935664512] [WARNING] Duplicate GeneSet member: 653720
[1771935664513] [WARNING] Duplicate GeneSet member: 124906683
[1771935664513] [WARNING] Duplicate GeneSet member: 221178
[1771935664515] [WARNING] Duplicate GeneSet member: 348840
[1771935664515] [WARNING] Duplicate GeneSet member: 157739
[1771935664516] [WARNING] Duplicate GeneSet member: 207147
[1771935664516] [WARNING] Duplicate GeneSet member: 124906377
[1771935664518] [WARNING] Duplicate GeneSet member: 339416
[1771935664519] [WARNING] Duplicate GeneSet member: 10492
[1771935664519] [WARNING] Duplicate GeneSet member: 64145
[1771935664520] [WARNING] Duplicate GeneSet member: 124906683
[1771935664520] [WARNING] Duplicate GeneSet member: 80862
[1771935664521] [WARNING] Duplicate GeneSet member: 54984
[1771935664521] [WARNING] Duplicate GeneSet member: 132989
[1771935664521] [WARNING] Duplicate GeneSet member: 414245
[1771935664522] [WARNING] Duplicate GeneSet member: 8916
[1771935664523] [WARNING] Duplicate GeneSet member: 83737
[1771935664523] [WARNING] Duplicate GeneSet member: 440519
[1771935664524] [WARNING] Duplicate GeneSet member: 9782
[1771935664524] [WARNING] Duplicate GeneSet member: 286042
[1771935664524] [WARNING] Duplicate GeneSet member: 23081
[1771935664525] [WARNING] Duplicate GeneSet member: 1201
[1771935664525] [WARNING] Duplicate GeneSet member: 101927815
[1771935664526] [WARNING] Duplicate GeneSet member: 56257
[1771935664527] [WARNING] Duplicate GeneSet member: 6817
[1771935664527] [WARNING] Duplicate GeneSet member: 64881
[1771935664528] [WARNING] Duplicate GeneSet member: 79400
[1771935664528] [WARNING] Duplicate GeneSet member: 102723927
[1771935664528] [WARNING] Duplicate GeneSet member: 6284
[1771935664529] [WARNING] Duplicate GeneSet member: 29994
[1771935664529] [WARNING] Duplicate GeneSet member: 8622
[1771935664529] [WARNING] Duplicate GeneSet member: 114794
[1771935664530] [WARNING] Duplicate GeneSet member: 10242
[1771935664530] [WARNING] Duplicate GeneSet member: 339822
[1771935664531] [WARNING] Duplicate GeneSet member: 5143
[1771935664531] [WARNING] Duplicate GeneSet member: 653145
[1771935664532] [WARNING] Duplicate GeneSet member: 104266957
[1771935664532] [WARNING] Duplicate GeneSet member: 100652739
[1771935664545] [INFO] There were duplicate row identifiers in the specified ranked list. One id was arbitarilly choosen. Details are below.
<br>Generally this is OK but if you want to avoid this, edit your ranked list so that all row ids are unique
<br>
<br># of row ids in original dataset: 24336
<br># of row UNIQUE ids in original dataset: 24295
<br>The duplicates were
<br><pre>79166 445347 5664 653720 124906683 221178 348840
157739 207147 124906377 339416 10492 64145 80862
54984 132989 414245 8916 83737 440519 9782
286042 23081 1201 101927815 56257 6817 64881
79400 102723927 6284 29994 8622 114794 10242
339822 5143 653145 104266957 100652739 </pre>
to parse>/imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_input/keratinocyte.genesets.v2026.1.Hs.gmt< got: [/imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_input/keratinocyte.genesets.v2026.1.Hs.gmt]
[1771935664564] [INFO] Begun importing: GeneSetMatrix from: /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_input/keratinocyte.genesets.v2026.1.Hs.gmt
[1771935664575] [INFO] Using file '/imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_input/keratinocyte.genesets.v2026.1.Hs.gmt' with unknown version
java.net.UnknownHostException: gseaftp.broadinstitute.org
at java.base/java.net.AbstractPlainSocketImpl.connect(Unknown Source)
at java.base/java.net.Socket.connect(Unknown Source)
at java.base/sun.net.ftp.impl.FtpClient.doConnect(Unknown Source)
at java.base/sun.net.ftp.impl.FtpClient.tryConnect(Unknown Source)
at java.base/sun.net.ftp.impl.FtpClient.connect(Unknown Source)
at java.base/sun.net.ftp.impl.FtpClient.connect(Unknown Source)
at java.base/sun.net.www.protocol.ftp.FtpURLConnection.connect(Unknown Source)
at java.base/sun.net.www.protocol.ftp.FtpURLConnection.getInputStream(Unknown Source)
at java.base/java.net.URL.openStream(Unknown Source)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.createInputStream(ParserFactory.java:1084)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.createInputStream(ParserFactory.java:1112)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readChip(ParserFactory.java:500)
at org.gsea_msigdb.gsea/edu.mit.broad.vdb.chip.Chip.readDeepData(Chip.java:182)
at org.gsea_msigdb.gsea/edu.mit.broad.vdb.chip.Chip.getNumProbes(Chip.java:202)
at org.gsea_msigdb.gsea/xtools.gsea.ToolHelper.checkNonMixedSpecies(ToolHelper.java:69)
at org.gsea_msigdb.gsea/xtools.gsea.ToolHelper.validateMixedVersionAndSpecies(ToolHelper.java:94)
at org.gsea_msigdb.gsea/xtools.gsea.GseaPreranked.execute(GseaPreranked.java:96)
at org.gsea_msigdb.gsea/xtools.api.AbstractTool.module_main(AbstractTool.java:401)
at org.gsea_msigdb.gsea/org.genepattern.modules.GseaPrerankedWrapper.main(GseaPrerankedWrapper.java:245)
at org.gsea_msigdb.gsea/xapps.gsea.CLI.main(CLI.java:31)
java.lang.Exception: java.net.UnknownHostException: gseaftp.broadinstitute.org
at org.gsea_msigdb.gsea/edu.mit.broad.vdb.chip.Chip.readDeepData(Chip.java:187)
at org.gsea_msigdb.gsea/edu.mit.broad.vdb.chip.Chip.getNumProbes(Chip.java:202)
at org.gsea_msigdb.gsea/xtools.gsea.ToolHelper.checkNonMixedSpecies(ToolHelper.java:69)
at org.gsea_msigdb.gsea/xtools.gsea.ToolHelper.validateMixedVersionAndSpecies(ToolHelper.java:94)
at org.gsea_msigdb.gsea/xtools.gsea.GseaPreranked.execute(GseaPreranked.java:96)
at org.gsea_msigdb.gsea/xtools.api.AbstractTool.module_main(AbstractTool.java:401)
at org.gsea_msigdb.gsea/org.genepattern.modules.GseaPrerankedWrapper.main(GseaPrerankedWrapper.java:245)
at org.gsea_msigdb.gsea/xapps.gsea.CLI.main(CLI.java:31)
Caused by: java.net.UnknownHostException: gseaftp.broadinstitute.org
at java.base/java.net.AbstractPlainSocketImpl.connect(Unknown Source)
at java.base/java.net.Socket.connect(Unknown Source)
at java.base/sun.net.ftp.impl.FtpClient.doConnect(Unknown Source)
at java.base/sun.net.ftp.impl.FtpClient.tryConnect(Unknown Source)
at java.base/sun.net.ftp.impl.FtpClient.connect(Unknown Source)
at java.base/sun.net.ftp.impl.FtpClient.connect(Unknown Source)
at java.base/sun.net.www.protocol.ftp.FtpURLConnection.connect(Unknown Source)
at java.base/sun.net.www.protocol.ftp.FtpURLConnection.getInputStream(Unknown Source)
at java.base/java.net.URL.openStream(Unknown Source)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.createInputStream(ParserFactory.java:1084)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.createInputStream(ParserFactory.java:1112)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readChip(ParserFactory.java:500)
at org.gsea_msigdb.gsea/edu.mit.broad.vdb.chip.Chip.readDeepData(Chip.java:182)
... 7 more
[1771935664621] [INFO] Renaming rpt dir on error to: /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_output/error_keratinocyte._cmp01_C4_vs_C0_difB_.GseaPreranked.1771935664409

Lauro

[gsea-help]

Hi Lauro,

Thanks for letting us know. Our main developer is currently traveling, but we will look into this as soon as we can.

Helga

[David Eby]

Hi Lauro,

Can you confirm that the file at this path actually exists and is readable from the computer where GSEA is running?

/imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/Human_NCBI_Entrez_Gene_ID_MSigDB.v7.2.chip

If that's a networked drive, can you check whether it's properly mounted?

Reviewing the GSEA Desktop code, it should only attempt to load using the "gseaftp.broadinstitute.org" URL when the file is not found otherwise via a normal file read.  It is my understanding that Broad Institute retired "gseaftp.broadinstitute.org" some time ago, but this load wouldn't have worked in any case since the code would have attempted to use that full path on the remote (FTP) side.

This is admittedly a poor error message.  We've been trying to remove this type of "magic" auto-loading behavior from the code as we've had the opportunity; better to simply fail with a sane message in this case.  We're not actively working on an update right now, but I've captured this in our GitHub issues for a future release.

Thanks,

David

David Eby
www.gsea-msigdb.org

On Tue, Feb 24, 2026 at 6:52 AM Lauro Sumoy Van Dyck <lsum...@gmail.com> wrote:

Hi,

I have run into errors when attempting to execute gsea-cli.sh in linux. 

The same code was executed without a problem the last few days but now fails.

command used:

/home/labs/lslab/lsumoy/GSEA_Linux_4.3.3/gsea-cli.sh GSEAPreranked -gmx /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_input/keratinocyte.genesets.v2026.1.Hs.gmt -collapse Collapse -mode Max_probe -norm meandiv -nperm 1000 -rnk /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/cmp01_C4_vs_C0_prom_diffmeth_difB_entrez.rnk -scoring_scheme weighted -rpt_label keratinocyte._cmp01_C4_vs_C0_difB_ -chip /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/Human_NCBI_Entrez_Gene_ID_MSigDB.v7.2.chip -create_svgs false -include_only_symbols true -make_sets true -plot_top_x 20 -rnd_seed 149 -set_max 500 -set_min 15 -zip_report false -out /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_output

screen output with errors:

at org.gsea_msigdb.gsea/edu.mit.broad.vdb.chip.Chip.readDeepData(Chip./home/labs/lslab/lsumoy/GSEA_Linux_4.3.3/gsea-cli.sh GSEAPreranked -gmx /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_input/keratinocyte.genesets.v2026.1.Hs.gmt -collapse Collapse -mode Max_probe -norm meandiv -nperm 1000 -rnk /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/cmp01_C4_vs_C0_prom_diffmeth_difB_entrez.rnk -scoring_scheme weighted -rpt_label keratinocyte._cmp01_C4_vs_C0_difB_ -chip /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/Contrasts_final/Human_NCBI_Entrez_Gene_ID_MSigDB.v7.2.chip -create_svgs false -include_only_symbols true -make_sets true -plot_top_x 20 -rnd_seed 149 -set_max 500 -set_min 15 -zip_report false -out /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_outputjava:182)

... 7 more
[1771935664621] [INFO] Renaming rpt dir on error to: /imppc/labs/lslab/share/data/proc_data/20251219_CYoussif_LipotecLubrizol_EPIC/results/RnBeads/analysis/reports_final/GSEA/GSEA_output/error_keratinocyte._cmp01_C4_vs_C0_difB_.GseaPreranked.1771935664409

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[Lauro Sumoy Van Dyck]

Hi David,

Thanks for getting back. I just realised after reading your reply that I actually had moved that file to another directory and this explains the error message. Moving it back it now works perfectly.

That was an easy one to solve!

Thank you so much for your feedback.

Lauro