When I was running the EnTAP-nf with my nematode sequence, I replaced the plant refseq dataset with invertebrate refseq dataset from NCBI. The following error occurred.
No such file: /weka/data/lab/usr/05_entap/refseq/refseq_plant.protein.dmnd
-- Check script '/home/usr/.nextflow/assets/systemsgenetics/entapnf/workflows/entapnf.nf' at line: 219 or see '.nextflow.log' file for more details
The Error was solved when I change my invertebrate refseq dataset fasta file name to “refseq_plant.protein.dmnd”. In the nextflow script at line: 219, It should replace “db = [ file(params.data_refseq + "/refseq_plant.protein.dmnd", checkIfExists: true) ]” to ```db = [ file(params.data_refseq + "/*.dmnd", checkIfExists: true) ] ‘''
Best,
Ko
Command used and terminal output
nextflow run systemsgenetics/entapnf \
-resume \
-profile kamiak,singularity \
--batch_size 100 \
--input 05_entap/m_chitwoodi_clean.faa \
--data_sprot 01-input_data/functional_data/uniprot_sprot \
--data_refseq 05_entap/refseq \
--data_ipr 01-input_data/functional_data/interproscan/interproscan-5.36-75.0/data \
--enzyme_dat 01-input_data/functional_data/uniprot_sprot/enzyme.dat \
--max_cpus 100
##Output##
No such file: /weka/data/lab/usr/05_entap/refseq/refseq_plant.protein.dmnd
-- Check script '/home/usr/.nextflow/assets/systemsgenetics/entapnf/workflows/entapnf.nf' at line: 219 or see '.nextflow.log' file for more details
Relevant files
No response
System information
N E X T F L O W ~ version 21.10.6
systemsgenetics/entapnf v0.1.0
Description of the bug
When I was running the EnTAP-nf with my nematode sequence, I replaced the plant refseq dataset with invertebrate refseq dataset from NCBI. The following error occurred.
The Error was solved when I change my invertebrate refseq dataset fasta file name to “refseq_plant.protein.dmnd”. In the nextflow script at line: 219, It should replace “db = [ file(params.data_refseq + "/refseq_plant.protein.dmnd", checkIfExists: true) ]” to ```db = [ file(params.data_refseq + "/*.dmnd", checkIfExists: true) ] ‘''
Best,
Ko
Command used and terminal output
Relevant files
No response
System information
N E X T F L O W ~ version 21.10.6 systemsgenetics/entapnf v0.1.0