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epi2me-labs / wf-metagenomics

Metagenomic classification of long-read sequencing data
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Error: "Please make sure that the ref2taxid matches the reference." #107

Closed plycrsk closed 5 months ago

plycrsk commented 5 months ago

Operating System

macOS

Other Linux

No response

Workflow Version

v2.10.0-g671dff2

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-metagenomics --threads 8 --reference viral_library.fna --ref2taxid viral_prelim_map.tsv --fastq SQK-NBD114-24_barcode01 --exclude_host Nfu_20140520.dna.toplevel.fa --min_len 200 --min_read_qual 5 -profile singularity --classifier minimap2

Workflow Execution - CLI Execution Profile

None

What happened?

I'm having the same issues as #80

reference file example:

kraken:taxid|1965238|NC_034217.1 Pityohyphantes rubrofasciatus iflavirus isolate UW1, complete genome GTTATGACATTAGCTATTTAAACTCACTGTTTACATGTTTACTTAGTTATTCTATTATAA GAGATTTATCCACTTTCCTTTTCAATTTTGGATAGAAATTTATATAATTTCCCTATTTTA AAATAATCTCAAGGTTTTAAACCTCTTTAATTAGGACTGAAATGATTTTATTATGAAAAG TGTTTACACGCTTATTAATTTTAAATATTGTTTCTAAGAATTTAGATAATGTACCCCTAT

ref2taxid:

kraken:taxid|1965238|NC_034217.1 1965238 kraken:taxid|1690428|NC_042052.1 1690428 kraken:taxid|2660689|NC_074749.1 2660689 kraken:taxid|1476886|NC_024215.1 1476886 kraken:taxid|2560315|NC_025361.1 2560315 kraken:taxid|1048854|NC_033830.1 1048854 kraken:taxid|1048854|NC_033847.1 1048854 kraken:taxid|1048854|NC_033831.1 1048854 kraken:taxid|1922553|NC_032592.1 1922553 kraken:taxid|1923593|NC_033137.1 1923593

Length of files are the same and IDs are identical:

wc -l viral_prelim_map.tsv 18640 viral_prelim_map.tsv

grep '>' viral_library.fna | wc -l 18640

I get the same error as above the other users posted:

Error: The reference kraken:taxid|2786405|NC_074583.1 is not found in your ref2taxid file. Please make sure that the ref2taxid matches the reference. If your input are bam files, make sure that the ref2taxid matches the reference used for the mapping step.

This ID is in ref2taxid and matches.

Relevant log output

Error: The reference kraken:taxid|2786405|NC_074583.1 is not found in your ref2taxid file.
Please make sure that the ref2taxid matches the reference.
If your input are bam files, make sure that the ref2taxid matches
the reference used for the mapping step.

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

plycrsk commented 5 months ago

Resolved. issues with /t spacing and white space.