intermine / intermine/intermine-scripts
Download script - NCBI fasta - delete rubbish files from download
- Dominant language
- PLpgSQL
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Description
Here are the files we do not want:
```
rm hs_ref_GRCh38.p12_unlocalized.fa hs_ref_GRCh38.p12_unlocalized.mfa hs_ref_GRCh38.p12_unplaced.fa hs_ref_GRCh38.p12_unplaced.mfa
```
Here's the error:
```
Caused by: java.lang.RuntimeException: Couldn't find chromosome identifier ref|NT_187396.1| Homo sapiens unplaced genomic scaffold, GRCh38.p12 Primary Assembly HSCHRUN_RANDOM_100
at org.intermine.bio.dataconversion.NCBIFastaLoaderTask.getIdentifier(NCBIFastaLoaderTask.java:53)
at org.intermine.bio.dataconversion.FastaLoaderTask.processSequence(FastaLoaderTask.java:320)
at org.intermine.bio.dataconversion.FastaLoaderTask.processFile(FastaLoaderTask.java:240)
at org.intermine.task.FileDirectDataLoaderTask.process(FileDirectDataLoaderTask.java:50)
at org.intermine.bio.dataconversion.FastaLoaderTask.process(FastaLoaderTask.java:170)
at org.intermine.task.DirectDataLoaderTask.execute(DirectDataLoaderTask.java:168)
at org.intermine.bio.dataconversion.FastaLoaderTask.execute(FastaLoaderTask.java:215)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:293)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
... 38 more
```
We don't want unplaced features so delete these files on download.
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