Losing all data after filter step using SGA

Question

[jolespin]

Raw fastq > preprocess > index > correct > index = processed_reads.ec.fa (6.5 GB)

 

I've taken the processed_reads.ec.fa and ran the following command:

 

sga filter -k 31 processed_reads.ec.fa

 

stderr:

sga: QCProcess.cpp:233: DuplicateCheckResult QCProcess::performDuplicateCheck(const SequenceWorkItem&): Assertion `fwdIntervals.interval[0].isValid() || rcIntervals.interval[0].isValid()' failed.

 

 

stdout:

...

[sga] Processed 8000000 sequences (912.782961s elapsed)

[sga] Processed 8050000 sequences (918.024303s elapsed)

[sga] Processed 8100000 sequences (925.718005s elapsed)

[sga] Processed 8150000 sequences (932.858792s elapsed)

Abort (core dumped)

 

 

The output files were:

processed_reads.ec.filter.pass.fa (1.4 MB)

processed_reads.ec.discard.fa (2.0 GB)

 

Does anyone know what's happening? What are these errors? I've tried different thread sizes and different kmer sizes and have not seen any significant improvements...

Answer 1

[jolespin]

Needed the BWT file from the reindexing step