Could not find <WellSample> in input dataset. Will not add BioSamples to output XMLs

Question

[Ric]

Hi, After merging CCS Bam files and ran lim I got the below warings:

> dataset create --force --type ConsensusReadSet --name ccs_combined ccs_combined.consensusreadset.xml m54105_171201_020331.ccs.bam m54105_171201_121745.ccs.bam
> lima --isoseq --dump-clips -j 8 ccs_combined.consensusreadset.xml primers.fasta ccs_combined.bam
| 20220202 03:17:27.902 | WARN | Could not find <WellSample> in input dataset. Will not add BioSamples to output XMLs
| 20220202 03:17:27.903 | WARN | Can't forward external resources if more than one input BAM is present
| 20220202 03:17:27.922 | WARN | Can't forward external resources if more than one input BAM is present
| 20220202 03:17:27.922 | WARN | Could not find <WellSample> in input dataset. Will not add BioSamples to output XMLs

Content of ccs_combined.consensusreadset.xml:

<?xml version="1.0" encoding="utf-8"?>
<pbds:ConsensusReadSet CreatedAt="2022-02-02T03:17:27.921Z" MetaType="PacBio.DataSet.ConsensusReadSet" Name="ccs_combined (all samples)" Tags="barcoded,hidden" TimeStampedName="ccs_combined (all samples)-220202_031727922" UniqueId="22409840-fc5e-4b03-a259-82d8fb7a74d6" Version="3.0.1" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbdm="http://pacificbiosciences.com/PacBioDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbpn="http://pacificbiosciences.com/PacBioPartNumbers.xsd" xmlns:pbrk="http://pacificbiosciences.com/PacBioReagentKit.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd">
    <pbbase:ExternalResources>
        <pbbase:ExternalResource CreatedAt="2022-02-02T03:17:27.921Z" MetaType="PacBio.ConsensusReadFile.ConsensusReadBamFile" ResourceId="ccs_combined.5p--3p.bam" TimeStampedName="pacbio_consensusreadfile_consensusreadbamfile-220202_031727921" UniqueId="1ba23173-9c69-4f8d-a032-4131745f7618" Version="3.0.1">
            <pbbase:FileIndices>
                <pbbase:FileIndex CreatedAt="2022-02-02T03:17:27.921Z" MetaType="PacBio.Index.PacBioIndex" ResourceId="ccs_combined.5p--3p.bam.pbi" TimeStampedName="pacbio_index_pacbioindex-220202_031727921" UniqueId="540e8005-0808-4df9-8649-de781eb8c11d" Version="3.0.1" />
            </pbbase:FileIndices>
            <pbbase:ExternalResources>
                <pbbase:ExternalResource CreatedAt="2022-02-02T03:17:27.921Z" MetaType="PacBio.DataSet.ConsensusReadSet" ResourceId="ccs_combined.5p--3p.consensusreadset.xml" TimeStampedName="pacbio_dataset_consensusreadset-220202_031727921" UniqueId="ae27e572-5d5f-44da-bf4d-20dfe17b1dc8" Version="3.0.1" />
            </pbbase:ExternalResources>
        </pbbase:ExternalResource>
    </pbbase:ExternalResources>
    <pbds:DataSetMetadata>
        <pbds:TotalLength>23482154</pbds:TotalLength>
        <pbds:NumRecords>9496</pbds:NumRecords>
    </pbds:DataSetMetadata>
</pbds:ConsensusReadSet>

What did I miss?

Answer 1

[William Rowell]

lima is typically used on the output of individual SMRT Cells. Both warnings are due to running lima on a merged dataset from multiple SMRT Cells. These are just warnings and not errors, and they can be ignored if you're sticking to the command line for further analysis.