ielis
commented
3 months ago Hi @MiladEidi
Running
wget https://storage.googleapis.com/ielis/jannovar/v0.35/hg19_ucsc.serruns OK on my end, so I do not think there are any issues with the hosting. Your connectivity issues may be a result being behind a firewall (or similar), and, unfortunately, it is impossible for me to help you with that.
As a workaround, you can download the .ser files on another machine, and then copy them into the /mnt/c/Users/Milad/OneDrive/Desktop/lirical-cli-2.0.2/data folder.
Please have a look here, there are 4 URLs that are hosted on Google Cloud storage.
This is how the data folder should look like at the end:
data
├── hg19_refseq.ser
├── hg19_ucsc.ser
├── hg38_refseq.ser
├── hg38_ucsc.ser
├── hgnc_complete_set.txt
├── hp.json
├── mim2gene_medgen
└── phenotype.hpoaI'd be happy to help further if the above does not work, please let me know.
MiladEidi
Hi dear developers, when I try to download lirical's database it returns these:
(base) milad@DESKTOP-VI9DTD8:/mnt/c/Users/Milad/OneDrive/Desktop/lirical-cli-2.0.2$ java -jar lirical-cli-2.0.2.jar D SLF4J(I): Connected with provider of type [ch.qos.logback.classic.spi.LogbackServiceProvider]
| | | | | _/ | / \ | | | | | || |) || | | / \ | | | | | || _ < | | | / | |_ |___||| ___// ____|
LIkelihood Ratio Interpretation of Clinical AbnormaLities :: v2.0.2 ::
08:44:11.712 [main] INFO o.m.lirical.cli.cmd.DownloadCommand - Downloading data to /mnt/c/Users/Milad/OneDrive/Desktop/lirical-cli-2.0.2/data 08:44:12.221 [main] INFO o.m.biodownload.BioDownloaderBuilder - The builder validation is successful. 08:44:12.222 [main] INFO o.m.biodownload.BioDownloaderImpl - Cowardly refusing to download "hp.json" since we found it at "/mnt/c/Users/Milad/OneDrive/Desktop/lirical-cli-2.0.2/data/hp.json" 08:44:12.223 [main] INFO o.m.biodownload.BioDownloaderImpl - Cowardly refusing to download "phenotype.hpoa" since we found it at "/mnt/c/Users/Milad/OneDrive/Desktop/lirical-cli-2.0.2/data/phenotype.hpoa" 08:44:12.223 [main] INFO o.m.biodownload.BioDownloaderImpl - Cowardly refusing to download "hgnc_complete_set.txt" since we found it at "/mnt/c/Users/Milad/OneDrive/Desktop/lirical-cli-2.0.2/data/hgnc_complete_set.txt" 08:44:12.223 [main] INFO o.m.biodownload.BioDownloaderImpl - Cowardly refusing to download "mim2gene_medgen" since we found it at "/mnt/c/Users/Milad/OneDrive/Desktop/lirical-cli-2.0.2/data/mim2gene_medgen" 08:44:12.912 [main] ERROR o.m.biodownload.FileDownloader - Failed to downloaded file from storage.googleapis.com java.io.IOException: Server returned HTTP response code: 403 for URL: https://storage.googleapis.com/ielis/jannovar/v0.35/hg19_ucsc.ser at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:67) at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500) at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:484) at java.base/sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:2044) at java.base/sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:2039) at java.base/java.security.AccessController.doPrivileged(AccessController.java:569) at java.base/sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:2038) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1605) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1585) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224) at org.monarchinitiative.biodownload.FileDownloader.copyURLToFileThroughURL(FileDownloader.java:106) at org.monarchinitiative.biodownload.FileDownloader.copyURLToFile(FileDownloader.java:86) at org.monarchinitiative.biodownload.BioDownloaderImpl.downloadFileIfNeeded(BioDownloaderImpl.java:69) at org.monarchinitiative.biodownload.BioDownloaderImpl.download(BioDownloaderImpl.java:49) at org.monarchinitiative.lirical.cli.cmd.DownloadCommand.execute(DownloadCommand.java:57) at org.monarchinitiative.lirical.cli.cmd.BaseCommand.call(BaseCommand.java:31) at org.monarchinitiative.lirical.cli.cmd.DownloadCommand.call(DownloadCommand.java:21) at org.monarchinitiative.lirical.cli.cmd.BaseCommand.call(BaseCommand.java:18) at picocli.CommandLine.executeUserObject(CommandLine.java:2041) at picocli.CommandLine.access$1500(CommandLine.java:148) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461) at picocli.CommandLine$RunLast.handle(CommandLine.java:2453) at picocli.CommandLine$RunLast.handle(CommandLine.java:2415) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2273) at picocli.CommandLine$RunLast.execute(CommandLine.java:2417) at picocli.CommandLine.execute(CommandLine.java:2170) at org.monarchinitiative.lirical.cli.Main.main(Main.java:46) Caused by: java.io.IOException: Server returned HTTP response code: 403 for URL: https://storage.googleapis.com/ielis/jannovar/v0.35/hg19_ucsc.ser at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1993) at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1585) at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:529) at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:308) at org.monarchinitiative.biodownload.FileDownloader.connect(FileDownloader.java:149) at org.monarchinitiative.biodownload.FileDownloader.copyURLToFileThroughURL(FileDownloader.java:104) ... 16 common frames omitted 08:44:12.920 [main] ERROR o.m.biodownload.BioDownloaderImpl - Error downloading "hg19_ucsc.ser" from "https://storage.googleapis.com/ielis/jannovar/v0.35/hg19_ucsc.ser": ERROR: Problem downloading file: Server returned HTTP response code: 403 for URL: https://storage.googleapis.com/ielis/jannovar/v0.35/hg19_ucsc.ser 08:44:12.920 [main] ERROR o.m.lirical.cli.cmd.DownloadCommand - Error: ERROR: Problem downloading file: Server returned HTTP response code: 403 for URL: https://storage.googleapis.com/ielis/jannovar/v0.35/hg19_ucsc.ser org.monarchinitiative.biodownload.FileDownloadException: ERROR: Problem downloading file: Server returned HTTP response code: 403 for URL: https://storage.googleapis.com/ielis/jannovar/v0.35/hg19_ucsc.ser at org.monarchinitiative.biodownload.FileDownloader.copyURLToFileThroughURL(FileDownloader.java:136) at org.monarchinitiative.biodownload.FileDownloader.copyURLToFile(FileDownloader.java:86) at org.monarchinitiative.biodownload.BioDownloaderImpl.downloadFileIfNeeded(BioDownloaderImpl.java:69) at org.monarchinitiative.biodownload.BioDownloaderImpl.download(BioDownloaderImpl.java:49) at org.monarchinitiative.lirical.cli.cmd.DownloadCommand.execute(DownloadCommand.java:57) at org.monarchinitiative.lirical.cli.cmd.BaseCommand.call(BaseCommand.java:31) at org.monarchinitiative.lirical.cli.cmd.DownloadCommand.call(DownloadCommand.java:21) at org.monarchinitiative.lirical.cli.cmd.BaseCommand.call(BaseCommand.java:18) at picocli.CommandLine.executeUserObject(CommandLine.java:2041) at picocli.CommandLine.access$1500(CommandLine.java:148) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461) at picocli.CommandLine$RunLast.handle(CommandLine.java:2453) at picocli.CommandLine$RunLast.handle(CommandLine.java:2415) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2273) at picocli.CommandLine$RunLast.execute(CommandLine.java:2417) at picocli.CommandLine.execute(CommandLine.java:2170) at org.monarchinitiative.lirical.cli.Main.main(Main.java:46)
I tried it several times in different days, but the error still lasts... please help!