PUBLIC-1623 Diagnosis Attempt

[bio-boris]

The app is getting stuck on Could not read /data/RQCFilterData/human_genome/ref/index/1/bloom.serial . It appears that removing the human reads is running into problems.

So it looks like we need to change BBTools.java to be able to write the serial file to a new location, or to generate the bloom files ourselves and put them into the reference data folder, since that folder is being mounted via a ReadOnly mount

Running
find . | xargs grep -i -B5 -A10 "Could not read"

./bbmap/current/align2/BBMapAcc.java:				if(bloomSerial){System.out.println("Could not read "+serialPath+", generating filter from reference.");}
Binary file ./bbmap/current/align2/BBMapAcc.class matches
Binary file ./bbmap/current/align2/BBMap.class matches
./bbmap/current/align2/BBMapPacBioSkimmer.java:				if(bloomSerial){System.out.println("Could not read "+serialPath+", generating filter from reference.");}
./bbmap/current/align2/BBMap5.java:				if(bloomSerial){System.out.println("Could not read "+serialPath+", generating filter from reference.");}
Binary file ./bbmap/current/align2/BBMapPacBioSkimmer.class matches
./bbmap/current/align2/BBMap.java:				if(bloomSerial){System.out.println("Could not read "+serialPath+", generating filter from reference.");}
Binary file ./bbmap/current/align2/BBMap5.class matches
Binary file ./bbmap/current/align2/BBMapPacBio.class matches
./bbmap/current/align2/BBMapPacBio.java:				if(bloomSerial){System.out.println("Could not read "+serialPath+", generating filter from reference.");}

We would have to write a script to call that function and make the bloom.serial file

                if(makeBloomFilter){^M
                        String serialPath=RefToIndex.bloomLoc(build);^M
                        File serialFile=new File(serialPath);^M
                        if(bloomSerial && !RefToIndex.NODISK && serialFile.exists()){^M
                                bloomFilter=ReadWrite.read(BloomFilter.class, RefToIndex.bloomLoc(build), true);^M
                                t.stop("Loaded Bloom Filter: ");^M
                        }else{^M
                                if(bloomSerial){System.out.println("Could not read "+serialPath+", generating filter from reference.");}^M
                                bloomFilter=new BloomFilter(true, bloomFilterK, bloomFilterK, 1, bloomFilterHashes, bloomFilterMinHits, true);^M
                                t.stop("Made Bloom Filter: ");^M
                                if(bloomSerial && !RefToIndex.NODISK && !RefToIndex.FORCE_READ_ONLY){^M
//                                       && serialFile.canWrite()^M
                                        try {^M
                                                ReadWrite.writeObjectInThread(bloomFilter, serialPath, true);^M
                                                outstream.println("Writing Bloom Filter.");^M
                                        } catch (Throwable e) {^M
                                                e.printStackTrace();^M
                                                outstream.println("Can't Write Bloom Filter.");^M
                                        }^M
                                }^M
                        }^M
                        outstream.println(bloomFilter.filter.toShortString());^M
                        t.start();^M

(vi ./bbmap/current/align2/BBMapAcc.java)