Qiim2 help with the addition of my metadata sheet

I am new to Qiim2 I could not install Keemei and I keep having this error.

(qiime2-2019.10) eduroam-169-233-218-108:~ lizettgonzalez$ qiime tools inspect-metadata /Users/lizettgonzalez/Desktop/mouse/meta_data_mouse_8.csv

An error has been encountered:

Found unrecognized ID column name ‘sampleid,forward_fastq_file,reverse_fastq_file,treatment_group,litter,sex,c57bl6,description’ while searching for header. The first column name in the header defines the ID column, and must be one of these values:

Case-insensitive: ‘feature id’, ‘feature-id’, ‘featureid’, ‘id’, ‘sample id’, ‘sample-id’, 'sampleid’

Case-sensitive: ‘#OTU ID’, ‘#OTUID’, ‘#Sample ID’, ‘#SampleID’, 'sample_name’

There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org

Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2019.10/tutorials/metadata/

sampleid,forward_fastq_file,reverse_fastq_file,treatment_group,litter,sex,c57bl6,description

J077,16S-77_S30_L001_R1_001.fastq,16S-77_S30_L001_R2_001.fastq,Ctrl,JCB-08,Male,N,Ctrl

J079,16S-79_S31_L001_R1_001.fastq,16S-79_S31_L001_R2_001.fastq,Ctrl,JCB-08,Male,N,Ctrl

J081,16S-81_S32_L001_R1_001.fastq,16S-81_S32_L001_R2_001.fastq,Ctrl,JCB-08,Female,N,Ctrl

J082,16S-82_S33_L001_R1_001.fastq,16S-82_S33_L001_R2_001.fastq,PPE,JCB-09,Male,N,PPE

J083,16S-83_S34_L001_R1_001.fastq,16S-83_S34_L001_R2_001.fastq,PPE,JCB-09,Male,N,PPE

J086,16S-86_S35_L001_R1_001.fastq,16S-86_S35_L001_R2_001.fastq,PPE,JCB-09,Female,N,PPE

J087,16S-87_S36_L001_R1_001.fastq,16S-87_S36_L001_R2_001.fastq,PPE,JCB-09,Female,N,PPE

J090,16S-90_S37_L001_R1_001.fastq,16S-90_S37_L001_R2_001.fastq,PPE,JCB-10,Male,N,PPE

J095,16S-95_S38_L001_R1_001.fastq,16S-95_S38_L001_R2_001.fastq,PPE,JCB-10,Female,N,PPE

J096,16S-96_S39_L001_R1_001.fastq,16S-96_S39_L001_R2_001.fastq,PPE,JCB-10,Female,N,PPE

J134,16S-134_S47_L001_R1_001.fastq,16S-134_S47_L001_R2_001.fastq,Ctrl,JCB-19,Male,J,Ctrl

J135,16S-135_S48_L001_R1_001.fastq,16S-135_S48_L001_R2_001.fastq,Ctrl,JCB-19,Male,J,Ctrl

J139,16S-139_S49_L001_R1_001.fastq,16S-139_S49_L001_R2_001.fastq,Ctrl,JCB-19,Female,J,Ctrl

J141,16S-141_S50_L001_R1_001.fastq,16S-141_S50_L001_R2_001.fastq,Ctrl,JCB-19,Female,J,Ctrl

J142,16S-142_S40_L001_R1_001.fastq,16S-142_S40_L001_R2_001.fastq,PPE : Veh,JCB-20,Male,J,PPE : Veh

J144,16S-144_S41_L001_R1_001.fastq,16S-144_S41_L001_R2_001.fastq,PPE : Veh,JCB-20,Female,J,PPE : Veh

J145,16S-145_S42_L001_R1_001.fastq,16S-145_S42_L001_R2_001.fastq,PPE : Veh,JCB-20,Female,J,PPE : Veh

J147,16S-147_S55_L001_R1_001.fastq,16S-147_S55_L001_R2_001.fastq,PPE : Pro,JCB-21,Male,J,PPE : Pro

J148,16S-148_S56_L001_R1_001.fastq,16S-148_S56_L001_R2_001.fastq,PPE : Pro,JCB-21,Female,J,PPE : Pro

J149,16S-149_S57_L001_R1_001.fastq,16S-149_S57_L001_R2_001.fastq,PPE : Pro,JCB-21,Female,J,PPE : Pro

J189,16S-189_S43_L001_R1_001.fastq,16S-189_S43_L001_R2_001.fastq,PPE : Pro,JCB-28,Male,J,PPE : Pro

J190,16S-190_S44_L001_R1_001.fastq,16S-190_S44_L001_R2_001.fastq,PPE : Pro,JCB-28,Male,J,PPE : Pro

J192,16S-192_S45_L001_R1_001.fastq,16S-192_S45_L001_R2_001.fastq,PPE : Pro,JCB-28,Female,J,PPE : Pro

J193,16S-193_S46_L001_R1_001.fastq,16S-193_S46_L001_R2_001.fastq,PPE : Pro,JCB-28,Female,J,PPE : Pro

J194,16S-194_S58_L001_R1_001.fastq,16S-194_S58_L001_R2_001.fastq,PPE : Veh,JCB-29,Male,J,PPE : Veh

J196,16S-196_S59_L001_R1_001.fastq,16S-196_S59_L001_R2_001.fastq,PPE : Veh,JCB-29,Female,J,PPE : Veh

J197,16S-197_S60_L001_R1_001.fastq,16S-197_S60_L001_R2_001.fastq,PPE : Veh,JCB-29,Female,J,PPE : Veh

J199,16S-199_S51_L001_R1_001.fastq,16S-199_S51_L001_R2_001.fastq,Ctrl,CYH-189,Male,J,Ctrl

J200,16S-200_S52_L001_R1_001.fastq,16S-200_S52_L001_R2_001.fastq,Ctrl,CYH-189,Male,J,Ctrl

J201,16S-201_S53_L001_R1_001.fastq,16S-201_S53_L001_R2_001.fastq,Ctrl,CYH-189,Female,J,Ctrl

J202,16S-202_S54_L001_R1_001.fastq,16S-202_S54_L001_R2_001.fastq,Ctrl,CYH-189,Female,J,Ctrl

Welcome to the forum @Lizett_Gonzalez!

I have good news: this is an easy issue to fix. The issue is that your metadata file is comma-delimited CSV instead of tab-delimited TSV. Just replace the commas with tabs and you should be good to go!

(I can’t guarantee there won’t be other format issues, but just let me know if you run into other issues with this metadata file)

Good luck!

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I did try changing the file and this is the new error message
(qiime2-2019.10) eduroam-169-233-168-64:~ lizettgonzalez$ qiime metadata tabulate --m-input-file /Users/lizettgonzalez/Desktop/mouse/metadata_mouse.txt --o-visualization tabulated /Users/lizettgonzalez/Desktop/mouse/metadata_mouse -metadata.qzv
Usage: qiime metadata tabulate [OPTIONS]

Generate a tabular view of Metadata. The output visualization supports
interactive filtering, sorting, and exporting to common file formats.

Parameters:
–m-input-file METADATA…
(multiple The metadata to tabulate.
arguments will be
merged) [required]
–p-page-size INTEGER The maximum number of Metadata records to display
per page [default: 100]
Outputs:
–o-visualization VISUALIZATION
[required]
Miscellaneous:
–output-dir PATH Output unspecified results to a directory
–verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output if
execution is successful (silence is golden).
–citations Show citations and exit.
–help Show this message and exit.

                There was a problem with the command:                     

(1/1?) no such option: -m

sampleid forward_fastq_file reverse_fastq_file treatment_group litter sex c57bl6 description
J077 16S-77_S30_L001_R1_001.fastq 16S-77_S30_L001_R2_001.fastq Ctrl JCB_08 Male N Ctrl
J079 16S-79_S31_L001_R1_001.fastq 16S-79_S31_L001_R2_001.fastq Ctrl JCB_08 Male N Ctrl
J081 16S-81_S32_L001_R1_001.fastq 16S-81_S32_L001_R2_001.fastq Ctrl JCB_08 Female N Ctrl
J082 16S-82_S33_L001_R1_001.fastq 16S-82_S33_L001_R2_001.fastq PPE JCB_09 Male N PPE
J083 16S-83_S34_L001_R1_001.fastq 16S-83_S34_L001_R2_001.fastq PPE JCB_09 Male N PPE
J086 16S-86_S35_L001_R1_001.fastq 16S-86_S35_L001_R2_001.fastq PPE JCB_09 Female N PPE
J087 16S-87_S36_L001_R1_001.fastq 16S-87_S36_L001_R2_001.fastq PPE JCB_09 Female N PPE
J090 16S-90_S37_L001_R1_001.fastq 16S-90_S37_L001_R2_001.fastq PPE JCB_10 Male N PPE
J095 16S-95_S38_L001_R1_001.fastq 16S-95_S38_L001_R2_001.fastq PPE JCB_10 Female N PPE
J096 16S-96_S39_L001_R1_001.fastq 16S-96_S39_L001_R2_001.fastq PPE JCB_10 Female N PPE
J134 16S-134_S47_L001_R1_001.fastq 16S-134_S47_L001_R2_001.fastq Ctrl JCB_19 Male J Ctrl
J135 16S-135_S48_L001_R1_001.fastq 16S-135_S48_L001_R2_001.fastq Ctrl JCB_19 Male J Ctrl
J139 16S-139_S49_L001_R1_001.fastq 16S-139_S49_L001_R2_001.fastq Ctrl JCB_19 Female J Ctrl
J141 16S-141_S50_L001_R1_001.fastq 16S-141_S50_L001_R2_001.fastq Ctrl JCB_19 Female J Ctrl
J142 16S-142_S40_L001_R1_001.fastq 16S-142_S40_L001_R2_001.fastq PPE_Veh JCB_20 Male J PPE_Veh
J144 16S-144_S41_L001_R1_001.fastq 16S-144_S41_L001_R2_001.fastq PPE_Veh JCB_20 Female J PPE_Veh
J145 16S-145_S42_L001_R1_001.fastq 16S-145_S42_L001_R2_001.fastq PPE_Veh JCB_20 Female J PPE_veh
J147 16S-147_S55_L001_R1_001.fastq 16S-147_S55_L001_R2_001.fastq PPE_Pro JCB_21 Male J PPE_Pro
J148 16S-148_S56_L001_R1_001.fastq 16S-148_S56_L001_R2_001.fastq PPE_Pro JCB_21 Female J PPE_Pro
J149 16S-149_S57_L001_R1_001.fastq 16S-149_S57_L001_R2_001.fastq PPE_Pro JCB_21 Female J PPE_Pro
J189 16S-189_S43_L001_R1_001.fastq 16S-189_S43_L001_R2_001.fastq PPE_Pro JCB_28 Male J PPE_Pro
J190 16S-190_S44_L001_R1_001.fastq 16S-190_S44_L001_R2_001.fastq PPE_Pro JCB_28 Male J PPE_Pro
J192 16S-192_S45_L001_R1_001.fastq 16S-192_S45_L001_R2_001.fastq PPE_Pro JCB_28 Female J PPE_Pro
J193 16S-193_S46_L001_R1_001.fastq 16S-193_S46_L001_R2_001.fastq PPE_Pro JCB_28 Female J PPE_Pro
J194 16S-194_S58_L001_R1_001.fastq 16S-194_S58_L001_R2_001.fastq PPE_Veh JCB_29 Male J PPE_Veh
J196 16S-196_S59_L001_R1_001.fastq 16S-196_S59_L001_R2_001.fastq PPE_Veh JCB_29 Female J PPE_Veh
J197 16S-197_S60_L001_R1_001.fastq 16S-197_S60_L001_R2_001.fastq PPE_Veh JCB_29 Female J PPE_Veh
J199 16S-199_S51_L001_R1_001.fastq 16S-199_S51_L001_R2_001.fastq Ctrl CYH_189 Male J Ctrl
J200 16S-200_S52_L001_R1_001.fastq 16S-200_S52_L001_R2_001.fastq Ctrl CYH_189 Male J Ctrl
J201 16S-201_S53_L001_R1_001.fastq 16S-201_S53_L001_R2_001.fastq Ctrl CYH_189 Female J Ctrl
J202 16S-202_S54_L001_R1_001.fastq 16S-202_S54_L001_R2_001.fastq Ctrl CYH_189 Female J Ctrl

Maybe the issue is the space in this filename?

Metadata_Marilou.txt (2.9 KB)

I don’t think the issue is any longer in the contents of the file, I think it is just a typo in the command:

You added a space (I assume unintentionally) into the output filepath, so this is possibly causing this error. Try this instead:

qiime metadata tabulate \
  --m-input-file /Users/lizettgonzalez/Desktop/mouse/metadata_mouse.txt \
  --o-visualization /Users/lizettgonzalez/Desktop/mouse/metadata_mouse-metadata.qzv
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