nextflow/poreCov Error : Nout enough reads all samples, please investigate results/1.Read_quality

[bioinfo-ebiogen]

Hello, I used nextflow/poreCov analysis, But These error keeps occurs.

Command used

nextflow run replikation/poreCov --fastq_pass fastq_test/ -r 0.9.5 --rapid -profile local,docker

## when a process failed it looks like this:
executor >  local (13)
[3d/57e031] process > collect_fastq_wf:collect_fastq (1)              [100%] 1 of 1 ✔
[8d/b73b32] process > read_qc_wf:nanoplot (2)                         [100%] 3 of 3 ✔
[83/9e8c49] process > read_classification_wf:kraken2 (3)              [100%] 3 of 3 ✔
[a4/703e96] process > read_classification_wf:krona (3)                [100%] 3 of 3 ✔
[31/8e1d8f] process > artic_ncov_wf:filter_fastq_by_length (2)        [100%] 3 of 3 ✔
[-        ] process > artic_ncov_wf:artic_medaka                      -
[-        ] process > artic_ncov_wf:covarplot                         -
[-        ] process > determine_lineage_wf:pangolin                   -
[-        ] process > determine_mutations_wf:nextclade                -
[-        ] process > genome_quality_wf:president                     -
[-        ] process > genome_quality_wf:seqrs                         -
[-        ] process > rki_report_wf:rki_report                        -
[-        ] process > align_to_reference                              -
[-        ] process > create_summary_report_wf:plot_coverages         -
[-        ] process > create_summary_report_wf:summary_report_default -
Not enough reads in all samples, please investigate results/1.Read_quality
Could not generate any genomes, please check your reads results/1.Read_quality

When I tried, The error occured the point starting nanoplot OR artic_ncov. Two error pointed out "Not enough reads in all samples" at the same time. And the process does not working anymore, just stopped with those warning sign.(not red one!)

Actually, I tried this options.

nextflow run replikation/poreCov -r 0.9.5 -profile local,docker \ --update FALSE --primerV, V1200 --minLength, 500 --maxLength, 1500 --rapid, TRUE

More Context

Computer specs if you are running locally (not in the cloud or a cluster)

OPERATING_SYSTEM = Ubuntu 18.04 LTS THREADS = default option RAM = 31GB RAM

What can i do for gettting normal output? Could I change the sample data(.fastq.qz) files? Please Let me know if you have the solution.

Thank you!

[replikation]

this message only appears if the output of the "filter_fastq_by_length" process has no reads. you could reduce --minLength 500 to e.g. --minLength 50 just to check if your reads are too short. how many reads are in your fastq files/sequencing run?

[replikation]

e.g. what do the nanoplot figures in results/1.Read_quality say?

[replikation]

@DataSpott could it be a bug in relation to the --rapid flag and the collect_fastq_wf:collect_fastq ?

[bioinfo-ebiogen]

this message only appears if the output of the "filter_fastq_by_length" process has no reads. you could reduce --minLength 500 to e.g. --minLength 50 just to check if your reads are too short. how many reads are in your fastq files/sequencing run?

Thank you for your support! When I checked the reads of the input file(fastq.qz), one of the input files had a very short read counts.

Changing input file to another one enough read counts is good to solve this problem.

[bioinfo-ebiogen]

nd the collect_fastq_wf:collect_fastq ?

And Actually, It was my company's project to give a solution to another company a analysis steps convenient. They said All input files used rapid kit to analysis. So If I did not use rapid options, it occurs error. Maybe in this case, I thought rapid options does not affect bad result to this problem. :)

[bioinfo-ebiogen]

I really appreciate your help, again. Thank you, and Have a nice day!

[bioinfo-ebiogen]

I received the e-mail that mentioned the specific error be occured with using --rapid option && --fastq_pass method. When will be fixed this error? If you could let me know when it will be completed, Please reply or mail me.

E-mail : jepark@e-biogen.com

Thank you for your support.

[replikation]

hi, not really an error, i just set the default min length for the rapid option to 100. the next release will include this change. you can put this repository on "watch releases" then you get notification if a new release is available