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[E::idx_find_and_load] Could not retrieve index file for Singularity /NextFlow

Hi I am writing my first code is dsl2 Nextflow using Singularity container as below main.nf

 process pbc_varicall {
        publishDir "/data/shared/clinical/LongRead/Data/resources/"
        container 'docker://google/deepvariant:1.5.0'

        input:
        path bam
        output:
        file "*"
        path 'out_m84011_220902_175841_Chr20.vcf.gz'

        script:
        """
        run_deepvariant  --model_type PACBIO --ref ${params.ref_genome} --reads ${bam} --output_vcf ${params.data_input}out_m84011_220902_175841_Chr20.vcf.gz --num_shards 20 --regions chr20
        """
}

workflow {
        bam=channel.fromPath("${params.data_input}/m84011_220902_175841_Aln.bam")
        pbc_varicall(bam)
}

when i execute the above command with Absolute PATH for BAM file in Script section it works file, but if i pass as $bam from Input and Abs path from Workflow bam channel it gives following error

  `ValueError: FAILED_PRECONDITION: Cannot query without an index
  [E::idx_find_and_load] Could not retrieve index file for 'm84011_220902_175841_Aln.bam'

I have BAI FAI index files for Ref and BAM, i had same issue while passing $Ref thats fixed by passing ${params.ref_genome} instead of $ref from input channel

dsl2 nextflow singularity
• 2,974 views • link
written by Kiran Kiran

1 answer

You're passing in the bam, but not the bai file.

Options

  1. pass in the bai file (its a file, just like you do with your bam file)
  2. create a new bai in the process using samtools (might be slow)
• 0 views • link
written by colindaven colindaven

I already have Index file for BAM, how to pass bai to Script command as it takes only BAM

• 0 views • link
written by Kiran Kiran

Just make a second channel with the index and provide it to the process. Many ways of doing that, e.g. via a tuple to permanently have bam and bai in the same object/variable, but this here is the simplest:

input:
path bam
path bai

Then it gets staged and is available to the process.

• 0 views • link
written by ATpoint ATpoint

I tried with above but it doesnt work unless it is paired and passed to workflow as below then it works perfectly Channel.fromFilePairs('/data/shared/clinical/LongRead/Data/*_{Aln2.bam,Aln2.bam.bai}') .map { it[1] } .set { ch_bam_bai }

• 0 views • link
written by Kiran Kiran

from.path only takes BAM then script gives index error,, So it need to be paired if one wants to pass in Workflow,, if direct BAM path is given in script: it works, not throught workflow channel

• 0 views • link
written by Kiran Kiran

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