Closed royfrancis closed 1 year ago
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
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
@drpatelh this is the same underlying issue as in #129. Did the NCBI eutils change? 🤔
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
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
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.
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!
Description of the bug
PRJNA625551 id is not recognised by the pipeline. Perhaps I am using it incorrectly.
Command used and terminal output
Relevant files
No response
System information
Nextflow/21.10.6 nf-core/2.1