{"action":"opened","issue":{"url":"https://api.github.com/repos/ncbi/sra-tools/issues/42","repository_url":"https://api.github.com/repos/ncbi/sra-tools","labels_url":"https://api.github.com/repos/ncbi/sra-tools/issues/42/labels{/name}","comments_url":"https://api.github.com/repos/ncbi/sra-tools/issues/42/comments","events_url":"https://api.github.com/repos/ncbi/sra-tools/issues/42/events","html_url":"https://github.com/ncbi/sra-tools/issues/42","id":183995598,"number":42,"title":"fastq-dump on downloaded SRA file fails","user":{"login":"map2085","id":10247340,"avatar_url":"https://avatars.githubusercontent.com/u/10247340?v=3","gravatar_id":"","url":"https://api.github.com/users/map2085","html_url":"https://github.com/map2085","followers_url":"https://api.github.com/users/map2085/followers","following_url":"https://api.github.com/users/map2085/following{/other_user}","gists_url":"https://api.github.com/users/map2085/gists{/gist_id}","starred_url":"https://api.github.com/users/map2085/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/map2085/subscriptions","organizations_url":"https://api.github.com/users/map2085/orgs","repos_url":"https://api.github.com/users/map2085/repos","events_url":"https://api.github.com/users/map2085/events{/privacy}","received_events_url":"https://api.github.com/users/map2085/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-10-19T15:29:21Z","updated_at":"2016-10-19T15:29:21Z","closed_at":null,"body":"I downloaded an SRA file manually via wget:\r\n\r\n`wget  ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByRun/sra/ERR/ERR161/ERR161917/ERR161917.sra`\r\n\r\nThen I perform fastq-dump on the local file:\r\n\r\n`fastq-dump  ./ERR161917.sra`\r\n\r\nAnd it fails with error message:\r\n\r\n> 2016-10-19T14:52:50 fastq-dump.2.8.0 err: binary large object corrupt while reading binary large object within virtual database module - failed /tmp/740660.1.standard.q/485/data/ERR161917.sra\r\n> \r\n> =============================================================\r\n> An error occurred during processing.\r\n> A report was generated into the file '/home/map2085/ncbi_error_report.xml'.\r\n> If the problem persists, you may consider sending the file\r\n> to 'sra@ncbi.nlm.nih.gov' for assistance.\r\n> =============================================================\r\n\r\n\r\n\r\nThis happens for dozens of Run accessions.  However, for hundreds of other run accessions, the exact same above commands complete successfully.\r\n\r\nDisk space is not an issue (4 TB free, while these .sra files are < 5 GB each).  Memory is also very large ( > 8 GB)\r\n\r\n**Do not respond with the following:**\r\n\r\n- \"just use  `fastq-dump  <accession>` \"\r\n- \"just use `prefetch  <accession>` \"\r\n\r\nfastq-dump is supposed to work on local SRA files, as it says in the fastq-dump help page.  **Do not tell me to do it another way.**  It should work as it claims to.\r\n\r\n"}}
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