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main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file! #109

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main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!#109
@anuC

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@anuC
anuC
opened on Nov 6, 2025

Dear Developers,

I am having the following error while using the standalone version of the PepQuery. I would appreciate if you could have a look into it. Part of the error message is shown below. I am facing this error while accessing all the 48 indexed MS datasets.

2025-11-06 11:53:43 [INFO ] main.java.pg.PeptideSearchMT[search:418] - Step 2: candidate spectra retrieval and PSM scoring ...
2025-11-06 11:53:44 [INFO ] main.java.msio.MsdataMatch[get_all_indexed_ms_file:87] - Used CPUs: 32
2025-11-06 11:53:44 [INFO ] main.java.msio.MsdataMatch[get_all_indexed_ms_file:88] - Download 120 index MS/MS files ...
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
com.amazonaws.services.s3.model.AmazonS3Exception: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: G8826GZJDVWD0QER; S3 Extended Request ID: 0h4oySCwRGSUgj455p2+dXDz6LoXS18FdeLJbq+cAaix+W/YipRPBn0MFuuxjhan193FUJUl6lw=; Proxy: null), S3 Extended Request ID: 0h4oySCwRGSUgj455p2+dXDz6LoXS18FdeLJbq+cAaix+W/YipRPBn0MFuuxjhan193FUJUl6lw=
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleErrorResponse(AmazonHttpClient.java:1879)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleServiceErrorResponse(AmazonHttpClient.java:1418)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1387)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1157)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:814)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:781)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:755)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:715)
at com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:697)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:561)
at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:541)
at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5456)
at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5403)
at com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1372)
at com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1346)
at com.amazonaws.services.s3.AmazonS3Client.doesObjectExist(AmazonS3Client.java:1427)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at main.java.pg.S3Interface.download(S3Interface.java:54)
at main.java.msio.IndexFileDownloadWorker.download(IndexFileDownloadWorker.java:34)
at main.java.msio.IndexFileDownloadWorker.run(IndexFileDownloadWorker.java:23)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
com.amazonaws.services.s3.model.AmazonS3Exception: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: G88D2WHBMWAG0AZR; S3 Extended Request ID: KCc+2mbyOY/6p47IDlUlDlkluuCTW5CXWfuIGQVDAi8elFXxd4NC+klrd7kOe+JjteV8RLeVa5w=; Proxy: null), S3 Extended Request ID: KCc+2mbyOY/6p47IDlUlDlkluuCTW5CXWfuIGQVDAi8elFXxd4NC+klrd7kOe+JjteV8RLeVa5w=
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleErrorResponse(AmazonHttpClient.java:1879)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleServiceErrorResponse(AmazonHttpClient.java:1418)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1387)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1157)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:814)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:781)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:755)
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:715)
at com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:697)
at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:561)
at com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:541)
at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5456)
at com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:5403)
at com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1372)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1346)
at com.amazonaws.services.s3.AmazonS3Client.doesObjectExist(AmazonS3Client.java:1427)
at main.java.pg.S3Interface.download(S3Interface.java:54)
at main.java.msio.IndexFileDownloadWorker.download(IndexFileDownloadWorker.java:34)
at main.java.msio.IndexFileDownloadWorker.run(IndexFileDownloadWorker.java:23)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
com.amazonaws.services.s3.model.AmazonS3Exception: Forbidden (Service: Amazon S3; Status Code: 403; Error Code: 403 Forbidden; Request ID: G88CSVQY72KZ9NH6; S3 Extended Request ID: PmaC0ckg1FXOJkIJ10NyRjuKa21V4v1RBR9g89akLYyhadoO0p0EBEeLoAVQlYnw3iYcGRJyvXo=; Proxy: null), S3 Extended Request ID: PmaC0ckg1FXOJkIJ10NyRjuKa21V4v1RBR9g89akLYyhadoO0p0EBEeLoAVQlYnw3iYcGRJyvXo=
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleErrorResponse(AmazonHttpClient.java:1879)
2025-11-06 11:53:45 [ERROR] main.java.pg.S3Interface[download:65] - Error when retrieving MS/MS index file!
at com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleServiceErrorResponse(AmazonHttpClient.java:1418)

Many thanks in advance

Regards
Anu

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