Error while submitting files

[bitupan-2025]

Hi all,
I am using webin-cli-9.0.1. But while submitting files the following error is occurring repeatedly:
ERROR: Failed to connect to FTP server. Failed to upload files to server because of a system error.
Any Suggestion from anybody on this?

Thank You
Bitu

[daaaaande]

same here

[willboulton]

Hi - same here - using Webin-cli 9.0.1 I get an error about sample being null when accessing TaxID (see below). Version 9.0.0 seems to work great - and the changelog /release note does mention that the TaxID in Biosample schema was the code changed...

Would it be possible to fix or revert this? It's not a problem to use 9.0.0 but the bulk-cli tool pulls the latest version unfortunately!

Many thanks! Will

failed_validations.txt (only relevant snippet)

INFO : Your application version is 9.0.1
ERROR: Failed to initialise validator. Cannot invoke "uk.ac.ebi.ena.webin.cli.validator.reference.Sample.getTaxId()" because "sample" is null
INFO : Creating report file: /workdir/submissions/./webin-cli.report
[2025-12-18 16:41:59.628357] VALIDATION FAILED - /workdir/manifests/Manifest_MB-12_R1_001.fastq.txt

traceback in webin-cli report

2025-12-18T16:42:03 ERROR: Failed to initialise validator. Cannot invoke "uk.ac.ebi.ena.webin.cli.validator.reference.Sample.getTaxId()" because "sample" is null
uk.ac.ebi.ena.webin.cli.WebinCliException: Failed to initialise validator. Cannot invoke "uk.ac.ebi.ena.webin.cli.validator.reference.Sample.getTaxId()" because "sample" is null
        at uk.ac.ebi.ena.webin.cli.WebinCliException.systemError(WebinCliException.java:69)
        at uk.ac.ebi.ena.webin.cli.WebinCliExecutor.readManifest(WebinCliExecutor.java:94)
        at uk.ac.ebi.ena.webin.cli.WebinCli.execute(WebinCli.java:283)
        at uk.ac.ebi.ena.webin.cli.WebinCli.__main(WebinCli.java:122)
        at uk.ac.ebi.ena.webin.cli.WebinCli.main(WebinCli.java:90)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:569)
        at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
        at org.springframework.boot.loader.Launcher.launch(Launcher.java:108)
        at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
        at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:65)
Caused by: java.lang.NullPointerException: Cannot invoke "uk.ac.ebi.ena.webin.cli.validator.reference.Sample.getTaxId()" because "sample" is null
        at uk.ac.ebi.ena.webin.cli.service.SampleService.isBiosamplesSampleValid(SampleService.java:225)
        at uk.ac.ebi.ena.webin.cli.service.SampleService.getSample(SampleService.java:147)
        at uk.ac.ebi.ena.webin.cli.manifest.processor.metadata.SampleProcessor.lambda$getSample$0(SampleProcessor.java:129)
        at uk.ac.ebi.ena.webin.cli.utils.ExceptionUtils.executeWithRestExceptionHandling(ExceptionUtils.java:49)
        at uk.ac.ebi.ena.webin.cli.manifest.processor.metadata.SampleProcessor.getSample(SampleProcessor.java:128)
        at uk.ac.ebi.ena.webin.cli.manifest.processor.metadata.SampleProcessor.process(SampleProcessor.java:81)
        at uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.lambda$validateFields$19(ManifestReader.java:585)
        at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
        at uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.validateFields(ManifestReader.java:578)
        at uk.ac.ebi.ena.webin.cli.manifest.ManifestReader.readManifest(ManifestReader.java:170)
        at uk.ac.ebi.ena.webin.cli.WebinCliExecutor.readManifest(WebinCliExecutor.java:87)
        ... 11 common frames omitted

command printed to be used (from the bulk submission tool)

****************************************************************************************************
Command to be executed:mkdir -p /workdir/manifests/Manifest_MB-12_R1_001.fastq-report && java -jar /webin-cli.jar -co
ntext reads -userName Webin-73688 -password jPtjjVJ!ZLVM6c6 -manifest /workdir/manifests/Manifest_MB-12_R1_001.fastq.
txt -inputDir /workdir -outputDir /workdir/submissions -submit -test
****************************************************************************************************