Charles H. Langley
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Activity overview
Latest activity by Charles H. Langley-
Charles H. Langley created a post,
Backing Up GenomicDBs ?
AnsweredIs there a recommended method to backup GenomicDBs? Is tar -czf target_DB.tar.gz target_DB/ appropriate? Cheers, Chuck
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Charles H. Langley commented,
One added item, the directory listing from the DB: (notice the permissions, should they matter). | => lltotal 2.7M-rwxrwx--- 1 sasha radusr 0 2020-04-20-14:02 __tiledb_workspace.tdb-rwxrwx--- 1 sas...
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Charles H. Langley commented,
Bug Report Re: GenomicsDBException: Duplicate sample name found: CH Langley 2Sept2020 Ah - interesting. Yes, if you don't mind uploading the callset.json and callset.json.fragmentlist as ...
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Charles H. Langley commented,
"SSC00007" in not in either callset.json or in callset.json.inc.backup . Thanks, Chuck
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Charles H. Langley commented,
contents of DB_chr1/: -rwxrwx--- 1 sasha radusr 0 2020-04-20-14:02 __tiledb_workspace.tdb-rwxrwx--- 1 sasha radusr 308K 2020-04-20-14:02 vcfheader.vcf-rwxrwx--- 1 sasha radusr 286K 2020-04-20-14:02...
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Charles H. Langley commented,
Hello Genevieve: "running this is parallel" ? I am not sure what level of parallelization to which you refer. The previous commands included multithreading as in "--reader-threads 12 \" It also i...
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Charles H. Langley commented,
We did upgrade to gatk V4.1.8.1. But the same error appears, "org.genomicsdb.exception.GenomicsDBException: Duplicate sample" Thanks for any help. Cheers, Chuck
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Charles H. Langley created a post,
.GenomicsDBException: Duplicate sample name found:
Hello: We have run into the GenomicsDBImport error: "org.genomicsdb.exception.GenomicsDBException: Duplicate sample name found" on our attempts to update DBs. Below is (first) a command, followed...
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Charles H. Langley commented,
OK
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Charles H. Langley commented,
Thanks for the quick response. This is not likely to be our issue, since we are not now using the sample_name_map_file option. We have a large DB created in a single run. Now we are trying to add ...