Hi Kos, I take you up on your challenge ;) However I don't know if this will fix it.
On Tue, Oct 7, 2014 at 11:31 PM, Konstantinos Mavrommatis < [email protected]> wrote: > > <val>sailfish quant --index > /reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex --libtype > 'T=PE:O=><:S=AS' -1 <(gunzip -c > /gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HP1_3_R1.fastq.gz) > -2 <(gunzip -c > /gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HP1_3_R2.fastq.gz) > -o > /gpfs/archive/RED/DA0000072/RNA-Seq/Processed/Sailfish-transcriptCounts/HP1_3.Sailfish.txt > -p 8 --no_bias_correct </val> > OK, the code above is what you intially pasted... > > <val>sailfish quant --index > /reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex --libtype > *'T=PE:O=><:S=AS'* -1 <(gunzip -c > /gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HP1_3_R1.fastq.gz) > -2 <(gunzip -c > /gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HP1_3_R2.fastq.gz) > -o > /gpfs/archive/RED/DA0000072/RNA-Seq/Processed/Sailfish-transcriptCounts/HP1_3.Sailfish.txt > -p 8 --no_bias_correct </val> > The code above is what you pasted once you had escaped everything. Did you do this manually? I get a different output which I've pased below 1sailfish quant --index /reference/v1/Homo-sapiens/GRCh37.p12/SailFishIndex --libtype *'T=PE:O=><:S=AS'* -1 <(gunzip -c /gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HP1_3_R1.fastq.gz) -2 <(gunzip -c /gpfs/archive/RED/DA0000072/RNA-Seq/RawData/FastqFiles/HP1_3_R2.fastq.gz) -o /gpfs/archive/RED/DA0000072/RNA-Seq/Processed/Sailfish-transcriptCounts/HP1_3.Sailfish.txt -p 8 --no_bias_correct Please notice the difference in the part which I have boldened. Can you try reingesting and see if your come up donald trumps? > > org.apache.oodt.cas.filemgr.structs.exceptions.IngestException: exception > ingesting product: [A1_1.Sailfish.sfish]: Message: Failed to ingest product > [org.apache.oodt.cas.filemgr.structs.Product@7c1ba98b] : > java.lang.Exception: > org.apache.oodt.cas.filemgr.structs.exceptions.CatalogException: Error > ingesting product [org.apache.oodt.cas.filemgr.structs.Product@5d3f1d87] > : HTTP method failed: HTTP/1.1 400 Bad Request > BTW, you also have AGAIN highlighted the horrible opaque Product objects we get as Exception output. I logged an issue for this last week. https://issues.apache.org/jira/browse/OODT-755 We need to fix this and I will try my damdest to hack it at the weekend. Thanks Lewis
