Alpha rarefaction error: "No such file or directory: %20area.jsonp"

[anna.abbey]

Hi QIIME 2 team,

I am encountering an error when running the qiime diversity alpha-rarefaction command. Below is the exact command and error message

qiime diversity alpha-rarefaction \

--i-table dada2_table_filt_contam_unclass_removed.qza \

--p-max-depth 1929 \

--p-steps 20 \

--i-phylogeny asvs-tree.qza \

--m-metadata-file Abbeyv4v5_sample_metadata.tsv \

--o-visualization rarefaction_curves.qzv

Plugin error from diversity:

"[Errno 2] No such file or directory: '/var/folders/vh/7cjr4nrx0wncjbk6vrqfvxn80000gn/T/qiime2-temp-privxcyn/shannon-neighbourhood/%20area.jsonp' "

"Debug info has been saved to /var/folders/vh/7cjr4nrx0wncjbk6vrqfvxn80000gn/T/qiime2-q2cli-err-ud78yc2g.log"

I would appreciate any guidance on resolving this issue.

Thank you so much in advance for your help!
Anna

[lizgehret]

Hi @anna.abbey,

Thanks for reaching out!

I suspect there's something going on with one of your metadata columns that's causing this problem - can you try running qiime tools inspect-metadata and share the output in your response?

Cheers

[anna.abbey]

Thank you for your assistance, This is my output after i run the code COLUMN NAME TYPE
======================= ===========
group categorical
date categorical
season categorical
forward sequence count numeric
reverse sequence count numeric
forward-primer-sequence categorical
reverse-primer-sequence categorical
forward-sequence-length categorical
reverse-sequence-length categorical
sample_type categorical
sequencing-type categorical
library-layout categorical
library-selection categorical
instrument categorical
platform categorical
center-name categorical
sample-ollection-date categorical
sample-season categorical
sample-volume-ml numeric
sample-depth categorical
study-site-name categorical
sample-environment-type categorical
latitude-longitude categorical
continent categorical
country categorical
province categorical
city categorical
neighbourhood/ area categorical
ph numeric
dn numeric
tc numeric
tn numeric
doc numeric
water-temperature numeric
air-temperature numeric
sample-treatment categorical
study-description categorical
======================= ===========
IDS: 22
COLUMNS: 37

[anna.abbey]

I already validated it with keemie

[ebolyen (Evan Bolyen)]

@anna.abbey

neighbourhood/ area

Looks like this is the problematic column.

The main issue is we aren't quoting / quite the way we would need to. So it looks like a directory to the filesystem, which isn't the case. I would recommend renaming that column from
neighbourhood/ area to something like neighbourhood_area.