Question: Losing all data after filter step using SGA
gravatar for jolespin
5.9 years ago by
United States
jolespin130 wrote:

Raw fastq > preprocess > index > correct > index = (6.5 GB)


I've taken the and ran the following command:


sga filter -k 31



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





[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: (1.4 MB) (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...

sga assemly kmer filter • 1.2k views
ADD COMMENTlink modified 5.8 years ago • written 5.9 years ago by jolespin130
gravatar for jolespin
5.8 years ago by
United States
jolespin130 wrote:

Needed the BWT file from the reindexing step

ADD COMMENTlink written 5.8 years ago by jolespin130
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