QIIME 1 Rarefaction plots - all metrics errors

Hi all,

So I am currently running QIIME 1 on a Oracle virtual machine (v5.1.26) for analysis of seagrass associated microbiome samples.

I am new to this QIIME business, so have a weak base when it comes to error solves.

The code im running is make_rarefaction_plots.py on data output from a refined USEARCHv11 OTU and denoising pipeline

alpha_rarefaction.py -i table_tax.biom -m SAMPLE_MAP.txt -o alphadiversity -p alpha_params.txt

I have created the alpha_params.txt file with desired metrics - those being: shannon,simpson,choa1,observed_otus
The following is then displayed:

*** ERROR RAISED DURING STEP: Rarefaction plot: All metrics
Command run was:
make_rarefaction_plots.py -i alphadiversity/alpha_div_collated/ -m SAMPLE_MAP.txt -o alphadiversity/alpha_rarefaction_plots/
Command returned exit status: 1

Traceback (most recent call last):
File “/usr/local/bin/make_rarefaction_plots.py”, line 229, in
File “/usr/local/bin/make_rarefaction_plots.py”, line 165, in main
File “/usr/local/lib/python2.7/dist-packages/qiime/colors.py”, line 519, in sample_color_prefs_and_map_data_from_options
mapping, headers, comments = get_map(options, data)
File “/usr/local/lib/python2.7/dist-packages/qiime/colors.py”, line 486, in get_map
data[‘map’] = parse_mapping_file(map_f)
File “/usr/local/lib/python2.7/dist-packages/qiime/parse.py”, line 135, in parse_mapping_file
raise QiimeParseError(“No header line was found in mapping file.”)
qiime.parse.QiimeParseError: No header line was found in mapping file.

The output folder 'alphadiversity/alpha_rarefaction_plots is then created but without any output files
I am certain that the mapping file has a header, which sadly is the only error output I can interpret…

Welcome all help,
Be kind : )

Hi @z0stera - I moved this post over to “Other Bioinformatics Tools,” and relabeled to indicate that this is a QIIME 1 question. Thanks!

@thermokarst thanks man!

Just so you know, QIIME 1 is no longer supported — you might not receive an answer to this question. We strongly recommend you upgrade to QIIME 2.