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Skip_quantification problem #106

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manburst opened this issue Feb 7, 2021 · 0 comments
Open

Skip_quantification problem #106

manburst opened this issue Feb 7, 2021 · 0 comments

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@manburst
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manburst commented Feb 7, 2021

Hello
I have an issue with running the pipeline. I just try manually to run the analysis with the test dataset from yours.
with this command
nextflow run nf-core/nanoseq \ --input samplesheet_bc_dx.csv \ --protocol cDNA \ --input_path /home/jirachote/test-datasets/fast5/barcoded \ --flowcell FLO-MIN106 \ --kit SQK-DCS109 \ --barcode_kit EXP-NBD103 \ -profile docker
give me an error
Quantification can only be performed if all samples in the samplesheet have the same reference fasta and GTF file." Please specify the '--skip_quantification' parameter if you wish to skip these steps.
even I add the reference to the spreadsheet, the same error will pop up.
so I have to add --skip_quantification then pipeline run successfully but the calibration (the third barcode) error in bigbed and bigwig step.
Now I tried with
./nextflow run nf-core/nanoseq --input samplesheet_bc_nodx.csv --protocol cDNA --input_path /home/jirachote/test-datasets/nonbarcoded/ --flowcell FLO-MIN106 --kit SQK-DCS108 --skip_demultiplexing -profile docker --max_cpus 2 --max_memory 6.GB --max_time 3.h
and again they give me
Quantification can only be performed if all samples in the samplesheet have the same reference fasta and GTF file." Please specify the '--skip_quantification' parameter if you wish to skip these steps.
This is weird because in the test spreadsheet of basecalling but no demultiplexing has only one reference.
again. I have to add --skip_quantification However, unlike with basecalling and demultiplexing (barcoded). This time the pipeline skip many steps
Here

executor >  local (7)
[63/8dee55] process > CHECK_SAMPLESHEET (samplesh... [100%] 1 of 1 ✔
[f0/a4bfc6] process > GUPPY (nonbarcoded)            [100%] 1 of 1 ✔
[b3/535422] process > PYCOQC (sequencing_summary.... [100%] 1 of 1 ✔
[01/8d25f2] process > NANOPLOT_SUMMARY (sequencin... [100%] 1 of 1 ✔
[-        ] process > NANOPLOT_FASTQ                 -
[-        ] process > FASTQC                         -
[-        ] process > GET_CHROM_SIZES                -
[-        ] process > GTF_TO_BED                     -
[-        ] process > MINIMAP2_INDEX                 -
[-        ] process > MINIMAP2_ALIGN                 -
[-        ] process > SAMTOOLS_SORT                  -
[-        ] process > BEDTOOLS_GENOMECOV             -
[-        ] process > UCSC_BEDGRAPHTOBIGWIG          -
[-        ] process > BEDTOOLS_BAMTOBED              -
[-        ] process > UCSC_BED12TOBIGBED             -
[8c/450417] process > OUTPUT_DOCUMENTATION           [100%] 1 of 1 ✔
[70/5874db] process > GET_SOFTWARE_VERSIONS          [100%] 1 of 1 ✔
[42/f0c6a3] process > MULTIQC (1)                    [100%] 1 of 1 ✔
-[nf-core/nanoseq] Pipeline completed successfully-

Please, could you give me any suggestions.

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