{"action":"created","issue":{"url":"https://api.github.com/repos/Illumina/Pisces/issues/1","repository_url":"https://api.github.com/repos/Illumina/Pisces","labels_url":"https://api.github.com/repos/Illumina/Pisces/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/Illumina/Pisces/issues/1/comments","events_url":"https://api.github.com/repos/Illumina/Pisces/issues/1/events","html_url":"https://github.com/Illumina/Pisces/issues/1","id":170299318,"number":1,"title":"Pisces requests FileCompression.dll in Unix system","user":{"login":"rmtsoa","id":16871194,"avatar_url":"https://avatars.githubusercontent.com/u/16871194?v=3","gravatar_id":"","url":"https://api.github.com/users/rmtsoa","html_url":"https://github.com/rmtsoa","followers_url":"https://api.github.com/users/rmtsoa/followers","following_url":"https://api.github.com/users/rmtsoa/following{/other_user}","gists_url":"https://api.github.com/users/rmtsoa/gists{/gist_id}","starred_url":"https://api.github.com/users/rmtsoa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmtsoa/subscriptions","organizations_url":"https://api.github.com/users/rmtsoa/orgs","repos_url":"https://api.github.com/users/rmtsoa/repos","events_url":"https://api.github.com/users/rmtsoa/events{/privacy}","received_events_url":"https://api.github.com/users/rmtsoa/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"tamsen","id":4562645,"avatar_url":"https://avatars.githubusercontent.com/u/4562645?v=3","gravatar_id":"","url":"https://api.github.com/users/tamsen","html_url":"https://github.com/tamsen","followers_url":"https://api.github.com/users/tamsen/followers","following_url":"https://api.github.com/users/tamsen/following{/other_user}","gists_url":"https://api.github.com/users/tamsen/gists{/gist_id}","starred_url":"https://api.github.com/users/tamsen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tamsen/subscriptions","organizations_url":"https://api.github.com/users/tamsen/orgs","repos_url":"https://api.github.com/users/tamsen/repos","events_url":"https://api.github.com/users/tamsen/events{/privacy}","received_events_url":"https://api.github.com/users/tamsen/received_events","type":"User","site_admin":false},"assignees":[{"login":"tamsen","id":4562645,"avatar_url":"https://avatars.githubusercontent.com/u/4562645?v=3","gravatar_id":"","url":"https://api.github.com/users/tamsen","html_url":"https://github.com/tamsen","followers_url":"https://api.github.com/users/tamsen/followers","following_url":"https://api.github.com/users/tamsen/following{/other_user}","gists_url":"https://api.github.com/users/tamsen/gists{/gist_id}","starred_url":"https://api.github.com/users/tamsen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tamsen/subscriptions","organizations_url":"https://api.github.com/users/tamsen/orgs","repos_url":"https://api.github.com/users/tamsen/repos","events_url":"https://api.github.com/users/tamsen/events{/privacy}","received_events_url":"https://api.github.com/users/tamsen/received_events","type":"User","site_admin":false}],"milestone":null,"comments":5,"created_at":"2016-08-10T00:01:42Z","updated_at":"2017-02-04T17:24:07Z","closed_at":null,"body":"Hi:\nI am trying to use Pisces to call rare variants in Unix system. I have already installed mono, and downloaded the latest Pisces_5_1_3. However, I kept receiving error message:\n\n8/9/2016 4:15:24 PM 1  ************\\* Starting **************\n8/9/2016 4:15:24 PM 1  Version:  5.1.3.60.\n8/9/2016 4:15:24 PM 1  Command-line arguments: .\n8/9/2016 4:15:24 PM 1  -B A921AC366.bam -g /Users/rtsoa/Desktop/Reference_Genome/b37_reference -f 0.0001 -fo False -b 20 -q 100 -c 1200 -s 0.5 -a 20 -F 20 -gVCF True.\n8/9/2016 4:15:24 PM 1  Exception reported:  \nSystem.Exception: Unable to process: FileCompression.dll ---> System.DllNotFoundException: FileCompression.dll\n  at (wrapper managed-to-native) SequencingFiles.Compression.SafeNativeMethods:UncompressBlock (byte[],uint,byte[],uint)\n  at SequencingFiles.BamReader.ReadBlock () <0x6c9ea8 + 0x00117> in <filename unknown>:0 \n  at SequencingFiles.BamReader.Read (System.Byte[]& data, UInt32 dataLength) <0x6c9ce0 + 0x000bf> in <filename unknown>:0 \n  at SequencingFiles.BamReader.LoadHeaderData () <0x6c9af0 + 0x0004b> in <filename unknown>:0 \n  at SequencingFiles.BamReader.Open (System.String filename) <0x6c9278 + 0x00293> in <filename unknown>:0 \n  at SequencingFiles.BamReader..ctor (System.String filename) <0x6c8e00 + 0x00033> in <filename unknown>:0 \n  at Pisces.Processing.WorkFactory.GetReferenceGenome (System.String genomePath) <0x6c8270 + 0x0015f> in <filename unknown>:0 \n  at Pisces.Program.Execute () <0x6c6e40 + 0x0009b> in <filename unknown>:0 \n  at Pisces.Program.Main (System.String[] args) <0x6bced8 + 0x0005b> in <filename unknown>:0 \n  --- End of inner exception stack trace ---.\n\nUnhandled Exception:\nSystem.Exception: Unable to process: FileCompression.dll ---> System.DllNotFoundException: FileCompression.dll\n  at (wrapper managed-to-native) SequencingFiles.Compression.SafeNativeMethods:UncompressBlock (byte[],uint,byte[],uint)\n  at SequencingFiles.BamReader.ReadBlock () <0x6c9ea8 + 0x00117> in <filename unknown>:0 \n  at SequencingFiles.BamReader.Read (System.Byte[]& data, UInt32 dataLength) <0x6c9ce0 + 0x000bf> in <filename unknown>:0 \n  at SequencingFiles.BamReader.LoadHeaderData () <0x6c9af0 + 0x0004b> in <filename unknown>:0 \n  at SequencingFiles.BamReader.Open (System.String filename) <0x6c9278 + 0x00293> in <filename unknown>:0 \n  at SequencingFiles.BamReader..ctor (System.String filename) <0x6c8e00 + 0x00033> in <filename unknown>:0 \n  at Pisces.Processing.WorkFactory.GetReferenceGenome (System.String genomePath) <0x6c8270 + 0x0015f> in <filename unknown>:0 \n  at Pisces.Program.Execute () <0x6c6e40 + 0x0009b> in <filename unknown>:0 \n  at Pisces.Program.Main (System.String[] args) <0x6bced8 + 0x0005b> in <filename unknown>:0 \n  --- End of inner exception stack trace ---\n  at Pisces.Program.Main (System.String[] args) <0x6bced8 + 0x0010b> in <filename unknown>:0 \n8/9/2016 4:15:24 PM 1  *******************\\* Ending *********************\n[ERROR] FATAL UNHANDLED EXCEPTION: System.Exception: Unable to process: FileCompression.dll ---> System.DllNotFoundException: FileCompression.dll\n  at (wrapper managed-to-native) SequencingFiles.Compression.SafeNativeMethods:UncompressBlock (byte[],uint,byte[],uint)\n  at SequencingFiles.BamReader.ReadBlock () <0x6c9ea8 + 0x00117> in <filename unknown>:0 \n  at SequencingFiles.BamReader.Read (System.Byte[]& data, UInt32 dataLength) <0x6c9ce0 + 0x000bf> in <filename unknown>:0 \n  at SequencingFiles.BamReader.LoadHeaderData () <0x6c9af0 + 0x0004b> in <filename unknown>:0 \n  at SequencingFiles.BamReader.Open (System.String filename) <0x6c9278 + 0x00293> in <filename unknown>:0 \n  at SequencingFiles.BamReader..ctor (System.String filename) <0x6c8e00 + 0x00033> in <filename unknown>:0 \n  at Pisces.Processing.WorkFactory.GetReferenceGenome (System.String genomePath) <0x6c8270 + 0x0015f> in <filename unknown>:0 \n  at Pisces.Program.Execute () <0x6c6e40 + 0x0009b> in <filename unknown>:0 \n  at Pisces.Program.Main (System.String[] args) <0x6bced8 + 0x0005b> in <filename unknown>:0 \n  --- End of inner exception stack trace ---\n  at Pisces.Program.Main (System.String[] args) <0x6bced8 + 0x0010b> in <filename unknown>:0 \n"},"comment":{"url":"https://api.github.com/repos/Illumina/Pisces/issues/comments/277460904","html_url":"https://github.com/Illumina/Pisces/issues/1#issuecomment-277460904","issue_url":"https://api.github.com/repos/Illumina/Pisces/issues/1","id":277460904,"user":{"login":"tamsen","id":4562645,"avatar_url":"https://avatars.githubusercontent.com/u/4562645?v=3","gravatar_id":"","url":"https://api.github.com/users/tamsen","html_url":"https://github.com/tamsen","followers_url":"https://api.github.com/users/tamsen/followers","following_url":"https://api.github.com/users/tamsen/following{/other_user}","gists_url":"https://api.github.com/users/tamsen/gists{/gist_id}","starred_url":"https://api.github.com/users/tamsen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tamsen/subscriptions","organizations_url":"https://api.github.com/users/tamsen/orgs","repos_url":"https://api.github.com/users/tamsen/repos","events_url":"https://api.github.com/users/tamsen/events{/privacy}","received_events_url":"https://api.github.com/users/tamsen/received_events","type":"User","site_admin":false},"created_at":"2017-02-04T17:24:07Z","updated_at":"2017-02-04T17:24:07Z","body":"Hi Rosemarie.\r\n\r\nThanks for your continued interest.\r\n\r\nSorry, we do not natively handle UMIs with Pisces. To keep the software clean, architecturally, it is a deliberate choice to handle UMIs upstream of Pisces. (IMO, UMI collapsing is a very different problem from Variant Calling).  Want you want to do is build a new bam with the UMIs taken into account, and feed that new bam to Pisces. Ie, make a new bam by collapsing all the sets of same-tagged reads into consensus reads. This will denoise your data and give you more accurate frequencies with Pisces.\r\n\r\nI will keep an eye out for an exe ready made for you to do this."}}
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