PRJN id not recognised

[royfrancis]

Description of the bug

PRJNA625551 id is not recognised by the pipeline. Perhaps I am using it incorrectly.

Command used and terminal output

nextflow run nf-core/fetchngs --input PRJNA625551 --outdir results --input_type sra

ERROR: Validation of pipeline parameters failed!
* --input: string [PRJNA602995] does not match pattern ^\S+\.txt$ (PRJNA602995)

Relevant files

No response

System information

Nextflow/21.10.6 nf-core/2.1

[Midnighter]

The ID should be in a text file that you provide as input. Please try:

echo PRJNA625551 > ids.txt

nextflow run nf-core/fetchngs --input ids.txt --outdir results --input_type sra

[royfrancis]

Now I get this:

Mixture of ids provided via --input: 
Please provide either SRA / ENA / DDBJ or Synapse ids!

nextflow run nf-core/fetchngs -c params.config

params.config

params.input = "ids.txt"
params.outdir = "results"
params.input_type = "sra"

params.max_cpus = 10
params.max_memory = 64.GB 
params.max_time = 4.h

process {
    withName: SRATOOLS_PREFETCH {
        ext.args = '--max-size 60g'
    }
}

ids.txt

PRJNA602995

[Midnighter]

@drpatelh this is the same underlying issue as in #129. Did the NCBI eutils change? 🤔

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?id=PRJNA602995&db=sra&rettype=runinfo&retmode=text

[royfrancis]

Also getting the same error with SRR ids.

Mixture of ids provided via --input: 
Please provide either SRA / ENA / DDBJ or Synapse ids!

ids.txt

SRR16299658

params.config

params.input = "ids.txt"
params.outdir = "results"
params.input_type = "sra"

params.max_cpus = 10
params.max_memory = 64.GB 
params.max_time = 15.h

nextflow run nf-core/fetchngs -c params.config -profile uppmax -resume --project snic2022-22-XXX

Nextflow/22.10.1
nf-core/2.6

[onertipaday]

Same issue here with SRR.

Mixture of ids provided via --input: Please provide either SRA / ENA / DDBJ or Synapse ids!

ids.txt

SRR8916053 SRR8916054

System Info

N E X T F L O W/ version 22.10.5 build 5840 nf-core/fetchngs v1.9-g084e5ef

[drpatelh]

The id (SRR16299658) from this comment works for me @royfrancis :

[02/fce925] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR16299658)             [100%] 1 of 1 ✔
[06/fa6ff4] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)                       [100%] 1 of 1 ✔
[b2/e4f24f] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX12578374_SRR16299658) [100%] 1 of 1 ✔
[0b/11faf1] process > NFCORE_FETCHNGS:SRA:SRA_MERGE_SAMPLESHEET                        [100%] 1 of 1 ✔
[6a/b19b80] process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                      [100%] 1 of 1 ✔
[e0/7b8500] process > NFCORE_FETCHNGS:SRA:CUSTOM_DUMPSOFTWAREVERSIONS (1)              [100%] 1 of 1 ✔
-[nf-core/fetchngs] Pipeline completed successfully-

The ids (SRR8916053, SRR8916054) from this comment work for me too @onertipaday:

[f9/f65fc8] process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR8916054)            [100%] 2 of 2 ✔
[f3/4cf125] process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (2)                     [100%] 2 of 2 ✔
[7c/d1b381] process > NFCORE_FETCHNGS:SRA:SRA_TO_SAMPLESHEET (SRX5697508_SRR8916054) [100%] 2 of 2 ✔
[e0/5d0c57] process > NFCORE_FETCHNGS:SRA:SRA_MERGE_SAMPLESHEET                      [100%] 1 of 1 ✔
[4b/c47018] process > NFCORE_FETCHNGS:SRA:MULTIQC_MAPPINGS_CONFIG                    [100%] 1 of 1 ✔
[3e/26913d] process > NFCORE_FETCHNGS:SRA:CUSTOM_DUMPSOFTWAREVERSIONS (1)            [100%] 1 of 1 ✔
-[nf-core/fetchngs] Pipeline completed successfully-

Command I used:

nextflow run . \
    --input ids.txt \
    -profile docker \
    --skip_fastq_download \
    --outdir ./results \

Not sure why this was happening but it might be worth re-trying after we have released v1.10.0. If the problem persists please feel free to re-open or create a new issue if unrelated.

[amnahsiddiqa]

ids_list.csv Hi team- So I am still facing the same issue. I have my file attached here. my command looks like this nextflow run nf-core/fetchngs -c params.config -profile docker And my error:------------------------------------------------------ Mixture of ids provided via --input: SRR23679488 Please provide either SRA / ENA / GEO / DDBJ or Synapse ids!