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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.
The text was updated successfully, but these errors were encountered:
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 stepsHere
Please, could you give me any suggestions.
The text was updated successfully, but these errors were encountered: