#48 Minid is not respected in bbwrap

[Silas Kieser]

It seems to me minratio is not respeced in BBwrap!

java -ea -Xmx76G -Xms76G -cp /scratch/project_2004930/databases/conda_envs/5a4baf86020b282d4d0c60cb9a832949/opt/bbmap-38.92-0/current/ align2.BBWrap build=1 overwrite=true fastareadlen=500 nodisk=t ref=SAMEA103958167/SAMEA103958167_contigs.fasta in1=SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_R1.fastq.gz,SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_se.fastq.gz in2=SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_R2.fastq.gz,null trimreaddescriptions=t out=SAMEA103958167/sequence_alignment/SAMEA103958167.sam threads=8 pairlen=1000 pairedonly=t minid=0.9 mdtag=t xstag=fs nmtag=t sam=1.3 local=t ambiguous=best secondary=t saa=f maxsites=10 unpigz=t -Xmx76G
Executing align2.BBWrap [build=1, overwrite=true, fastareadlen=500, nodisk=t, ref=SAMEA103958167/SAMEA103958167_contigs.fasta, in1=SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_R1.fastq.gz,SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_se.fastq.gz, in2=SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_R2.fastq.gz,null, trimreaddescriptions=t, out=SAMEA103958167/sequence_alignment/SAMEA103958167.sam, threads=8, pairlen=1000, pairedonly=t, minid=0.9, mdtag=t, xstag=fs, nmtag=t, sam=1.3, local=t, ambiguous=best, secondary=t, saa=f, maxsites=10, unpigz=t, -Xmx76G]

Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, nodisk=t, trimreaddescriptions=t, threads=8, pairlen=1000, pairedonly=t, minid=0.9, mdtag=t, xstag=fs, nmtag=t, sam=1.3, local=t, ambiguous=best, secondary=t, saa=f, maxsites=10, unpigz=t, ref=SAMEA103958167/SAMEA103958167_contigs.fasta, in=SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_R1.fastq.gz, out=SAMEA103958167/sequence_alignment/SAMEA103958167.sam, in2=SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_R2.fastq.gz]
Version 38.92

Set threads to 8
Retaining first best site only for ambiguous mappings.
Executing dna.FastaToChromArrays2 [SAMEA103958167/SAMEA103958167_contigs.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=false, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=true]

Set genScaffoldInfo=true
Set genome to 1

Loaded Reference:       0.077 seconds.
Loading index for chunk 1-1, build 1
Indexing threads started for block 0-1
Indexing threads finished for block 0-1
Generated Index:        12.146 seconds.
Analyzed Index:         3.295 seconds.
Started output stream:  0.115 seconds.
Cleared Memory:         0.130 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 8 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7

   ------------------   Results   ------------------

Genome:                 1
Key Length:             13
Max Indel:              16000
Minimum Score Ratio:    0.56
Mapping Mode:           normal
Reads Used:             67903922        (7675723086 bases)

Mapping:                1714.929 seconds.
Reads/sec:              39595.75
kBases/sec:             4475.82


Pairing data:           pct pairs       num pairs       pct bases          num bases

mated pairs:              0.0005%             159         0.0005%              34732
bad pairs:                0.0000%               0         0.0000%                  0
insert size avg:          188.48

[Silas Kieser]

I set minid=0.9 and minratio was 0.56

[Silas Kieser]

I see the same problem when running only bbmap.sh ref=Human/SAMEA103958167/SAMEA103958167_contigs.fasta in1=Human/SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_R1.fastq.gz in2=Human/SAMEA103958167/sequence_quality_control/SAMEA103958167_QC_R2.fastq.gz minid=0.9 nodisk out=mapped.sam -Xmx50g threads=5