Having issues with my file formats, can't find "Check Format" section

[Hugo_HAMMERLIN]

Hello,
I’m really new to this platform, and I tried using the univariate test on already processed data.
The only problem is that when I run the tool, I’m having this error: Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the ‘Check Format’ module in the ‘Quality Control’ section
And when I want to look for this format, I can’t find this section anywhere. Can someone help me please ? I’m pretty sure that’s because I’m using .csv formats, but I don’t know what to use then…
Thank you in advance for any response !

[jennaj]

Welcome, @Hugo_HAMMERLIN

@Hugo_HAMMERLIN

I’m having this error: Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the ‘Check Format’ module in the ‘Quality Control’ section
And when I want to look for this format, I can’t find this section anywhere.

Is this the tool you are looking for?

• Check Format Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files
• Maybe the server where you are working doesn’t host it. But I do see it at the UseGalaxy.eu server, here → Galaxy

@Hugo_HAMMERLIN

I’m pretty sure that’s because I’m using .csv formats, but I don’t know what to use then…

Galaxy will automatically convert csv to tabular format at runtime, or you can convert your data to tabular format directly. If you need to make a change, or inspect values directly, tabular will be easier.

• FAQ: Converting the file format or FAQ: Converting the datatype of a collection

From there, you can cut out columns of data, sort, get unique values, compare two or more lists of values, make format changes, etc with Text Manipulation tools.

• Examples → Hands-on: Data Manipulation Olympics / Data Manipulation Olympics / Introduction to Galaxy Analyses
• Or, you can use regular command line tools in an Interactive Environment. Examples when using GIEs.

Please let us know if this helps or not, and we can follow up more!

[Hugo_HAMMERLIN]

Hello,
First of all, thank you for your response, it helped me fixing some issues of my formated files
However, I have an issue that I can’t seem to get my head around, it’s about my variable metadata file, I have this error : Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 21 did not have 5 elements
Calls: readAndCheckF → read.table → scan
Execution halted
However, I have checked multiple times and I really do have 5 elements in that line. Moreover, I checked the other lines and all of them have 5 elements.
Did I do something wrong ? How can I fix it ?
Thank you in advance for any response
Hugo HAMMERLIN

[jennaj]

Hi @Hugo_HAMMERLIN

For this part

@Hugo_HAMMERLIN

line 21 did not have 5 elements

did you check that exact line or just the top of the file?

Common reasons are usually about extra whitespace in the file – space or tab or newline characters. But there could also be an unexpected header line that the tool is attempting to parse.

1. Check for an internal space in term values.

   A term like StormTrooper is great.
   A term like Storm Trooper will cause problems with most computational tools.
   Some tools will also accept Storm-Trooper (a dash character) but others prefer Storm_Trooper (an underscore character) and the manual for the tool will usually explain what is expected, or you can just try both and see what happens, then adjust if you get an error. Not using any special characters is usually easiest if you don’t care so much about the format.

2. Check for extra tabs between terms or trailing at the end of lines.

3. Check for extra newlines in the file. These will look like blank lines at the start of the file or at the end of the file, and maybe between data lines, and these might also contain more spaces and tabs!

4. Check for header lines. A tool will generally declare if a header line is expected or not, and how many lines that can be, the format (does it start with a # or not, is whitespace Ok or not), and some tool forms will have an extra option to check off for this being present/not.

5. Combinations of all of the above! Plus more exotic whitespace characters like a soft return.

If you find some problem, you can usually fix the data in Galaxy using the Text Manipulation tools I linked to above. See the Cheatsheet guide at the top to get started.

Please give this a try and if you get stuck, you can share back your file, explain what you think is going wrong and what you tried, and we can try to help more by suggesting tool/manipulation choices. Do this by sharing the history with the file and the failed manipulations. How to generate the link is in the banner of this forum.

Hope this helps and let us know if you solve this!

[Hugo_HAMMERLIN]

Hello,
I checked everything, and I still don’t understand why it doesn’t work
I removed the last column, as it could’ve been the issue, but no, now it says

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 21 did not have 4 elements
Calls: readAndCheckF -> read.table -> scan

I’m uploading the variable metadata here, because I really need help here… I tried looking at it with Notepad++ just so I can see all the characters, and I just see 4 columns…
I replaced somes spaces that I ignored with underscore
I also removed spaces that were hust before my tabulations
Now there’s only tabulations but it still didn’t work

Sample_ID	Variable_name	ClassFire_Sub_class	ClassFire_Parent_Level5
L-Alanine	L-Alanine	Amino_acids_peptides_and_analogues	Alanine_and_derivatives
L-Arginine	L-Arginine	Amino_acids_peptides_and_analogues 	L-alpha-amino_acids
L-Asparagine	L-Asparagine	Amino_acids_peptides_and_analogues	Asparagine_and_derivatives
L-aspartic_acid	L-aspartic_acid	Amino_acids_peptides_and_analogues	Aspartic_acid_and_derivatives
L-cysteine	L-cysteine	Amino_acids_peptides_and_analogues	Cysteine_and_derivatives
Glutamic_acid	Glutamic_acid	Amino_acids_peptides_and_analogues	Glutamic_acid_and_derivatives
Glutamine	Glutamine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Histidine	Histidine	Amino_acids_peptides_and_analogues	Histidine_and_derivatives
Isoleucine	Isoleucine	Amino_acids_peptides_and_analogues	Isoleucine_and_derivatives
Lysine	Lysine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Methionine	Methionine	_Amino_acids_peptides_and_analogues	Methionine_and_derivatives
Phenylalanine	Phenylalanine	Amino_acids_peptides_and_analogues	Phenylalanine_and_derivatives
Proline	Proline	Amino_acids_peptides_and_analogues	Proline_and_derivatives
Serine	Serine	Amino_acids_peptides_and_analogues	Serine_and_derivatives
L-Threonine	L-Threonine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
L-Tryptophan	L-Tryptophan	Indolyl_carboxylic_acids_and_derivatives	Indolyl_carboxylic_acids_and_derivatives
L-Tyrosine	L-Tyrosine	Amino_acids_peptides_and_analogues	Tyrosine_and_derivatives
L-Valine	L-Valine	Amino_acids_peptides_and_analogues	Valine_and_derivatives
L-Cystine	L-Cystine	Amino_acids_peptides_and_analogues	L-cysteine-S-conjugates
Adenosine_diphosphate	Adenosine_diphosphate	Purine_ribonucleotides	Purine_ribonucleoside_diphosphates
Deoxyadenosine_monophosphate	Deoxyadenosine_monophosphate	Purine_deoxyribonucleotides	Purine_2'-deoxyribonucleoside_monophosphates
cytidine	cytidine	Not_Available	Pyrimidine_nucleosides
Thymine	Thymine	Pyrimidines_and_pyrimidine_derivatives	Hydroxypyrimidines
Uridine_diphosphate	Uridine_diphosphate	Pyrimidine_ribonucleotides	Pyrimidine_ribonucleoside_diphosphates
Uracil	Uracil	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
IDP	IDP	Purine_ribonucleotides	Purine_ribonucleotides_diphosphates
Inosine	Inosine	Not_Available	Purine_nucleosides
Hypoxanthine	Hypoxanthine	Purines_and_purine_derivatives	Hypoxanthines
Xanthine	Xanthine	Purines_and_purine_derivatives	Xanthines
allantoic_acid	allantoic_acid	Amino_acids_peptides_and_analogues	N-carbamoyl-alpha_amino_acids
5-Hydroxyisourate	5-Hydroxyisourate	_Purines_and_purine_derivatives_	Xanthines
Cytidine_2'.3'-cyclic_phosphate	Cytidine_2',3'-cyclic_phosphate	Amino_acids_peptides_and_analogues	Peptides
Inosine_2'.3'-cyclic_phosphate	Inosine_2',3'-cyclic_phosphate	Cyclic_purine_nucleotides	2',3'-cyclic_purine_nucleotides
5.6-dihydrothymine	5,6-dihydrothymine	Pyrimidines_and_pyrimidine_derivatives_	Hydropyrimidines
Pyridoxamine_5'-phosphate	Pyridoxamine_5'-phosphate	Pyridoxamines	Pyridoxamine_5'-phosphates
Niacinamide	Niacinamide	Pyridinecarboxylic_acids_and_derivatives	Nicotinamides
Adenylsuccinic_acid	Adenylsuccinic_acid	Purine_ribonucleotides	Purine_ribonucleoside_monophosphates
NADPDP	Benzenediols	Catechols
NADD	Not_Available	(5'->5')-dinucleotides
Phosphate	Phosphate	Non-metal_phosphates	Non-metal_phosphates
diphosphate	diphosphate	Non-metal_pyrophosphates	Non-metal_pyrophosphates
D-Glucose	D-Glucose	Carbohydrates_and_carbohydrate_conjugates	Hexoses
glucose-1-phosphate	glucose-1-phosphate	Carbohydrates_and_carbohydrate_conjugates	Monosaccharide_phosphates
Glyceraldehyde_3-phosphate	Glyceraldehyde_3-phosphate	Carbohydrates_and_carbohydrate_conjugates	Glyceraldehyde-3-phosphates
2-Phosphoglycerate	2-Phosphoglycerate	Carbohydrates_and_carbohydrate_conjugates	Sugar_acids_and_derivatives
pyruvate	pyruvate	Keto_acids_and_derivatives	Alpha-keto_acids_and_derivatives
Lactic_acid	Lactic_acid	Alpha_hydroxy_acids_and_derivatives	Alpha_hydroxy_acids_and_derivatives
D-Maltose	D-Maltose	Carbohydrates_and_carbohydrate_conjugates	O-glycosyl_compounds
D-Ribose	D-Ribose	Carbohydrates_and_carbohydrate_conjugates	Pentoses
Rhamnose	Rhamnose	Carbohydrates_and_carbohydrate_conjugates	Hexoses
D-Arabitol	D-Arabitol	Carbohydrates_and_carbohydrate_conjugates	Sugar_alcohols
citrate	citrate	Tricarboxylic_acids_and_derivatives	Tricarboxylic_acids_and_derivatives
alpha-ketoglutarate	alpha-ketoglutarate	Gamma-keto_acids_and_derivatives	Gamma-keto_acids_and_derivatives
2-Keto-glutaramic_acid	2-Keto-glutaramic_acid	Short-chain_keto_acids_and_derivatives_	Short-chain_keto_acids_and_derivatives
succinate	succinate	Dicarboxylic_acids_and_derivatives	Dicarboxylic_acids_and_derivatives
fumarate	fumarate	Dicarboxylic_acids_and_derivatives 	Dicarboxylic_acids_and_derivatives 
Malate	Malate	Beta_hydroxy_acids_and_derivatives	Beta_hydroxy_acids_and_derivatives
Oxalacetic_acid	Oxalacetic_acid	Short-chain_keto_acids_and_derivatives	Short-chain_keto_acids_and_derivatives
2-Hydroxyglutarate	2-Hydroxyglutarate	Short-chain_hydroxy_acids_and_derivatives	Short-chain_hydroxy_acids_and_derivatives
ribose-1-phosphate	ribose-1-phosphate	Carbohydrates_and_carbohydrate_conjugates	Pentoses
Pyroglutamic_acid	Pyroglutamic_acid	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
ascorbate	ascorbate	Furanones	Butenolides
Dehydroascorbic_acid	Dehydroascorbic_acid	Gamma_butyrolactones	Gamma_butyrolactones
gamma-Glutamylcysteine	gamma-Glutamylcysteine	Amino_acids_peptides_and_analogues	N-acyl-alpha_amino_acids
Gamma-Glutamyl-Se-methylselenocysteine	Gamma-Glutamyl-Se-methylselenocysteine	Amino_acids_peptides_and_analogues	Dipeptides
gamma-Glutamylalanine	gamma-Glutamylalanine	Amino_acids_peptides_and_analogues	Dipeptides
Glutamylglutamine	Glutamylglutamine	Amino_acids_peptides_and_analogues	Dipeptides
Homocysteine	Homocysteine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Dimethylglycine	Dimethylglycine	Amino_acids_peptides_and_analogues_	Alpha_amino_acids
phosphoserine	phosphoserine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Ornithine	Ornithine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Citrulline	Citrulline	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Cadaverine	Cadaverine	Amines_	Monoalkylamines
Putrescine	Putrescine	Amines	Monoalkylamines
Spermidine	Spermidine	Amines	Dialkylamines
N-Acetylneuraminic_acid	N-Acetylneuraminic_acid	Carbohydrates_and_carbohydrate_conjugates	N-acylneuraminic_acids
N-Acetyl-glucosamine_1-phosphate	N-Acetyl-glucosamine_1-phosphate	Carbohydrates_and_carbohydrate_conjugates	N-acyl-alpha-hexosamines
?-D-xylan	?-D-xylan	Not_found_yet	Not_found_yet
Phosphocreatine	Phosphocreatine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
Creatine	Creatine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
Creatinine	Creatinine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
4-Acetamidobutanoic_acid	4-Acetamidobutanoic_acid	Amino_acids_peptides_and_analogues	Gamma_amino_acids_and_derivatives
N2-Acetylornithine	N2-Acetylornithine	Amino_acids_peptides_and_analogues	N-acyl-L-alpha-amino_acids
Guanidoacetic_acid	Guanidoacetic_acid	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
4-Hydroxyproline	4-Hydroxyproline	_Amino_acids_peptides_and_analogues	Proline_and_derivatives
N2-Succinyl-L-glutamic_acid_5-semialdehyde	N2-Succinyl-L-glutamic_acid_5-semialdehyde	Amino_acids_peptides_and_analogues	N-acyl-L-alpha-amino_acids
Pantothenol	Pantothenol	Fatty_amides	N-acyl_amines
Dihydrouracil	Dihydrouracil	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
Pantetheine	Pantetheine	Amino_acids_peptides_and_analogues	Beta_amino_acids_and_derivatives
Taurine	Taurine	Organosulfonic_acids_and_derivatives	Organosulfonic_acids
3-SULFOCATECHOL	3-SULFOCATECHOL	Not_found_yet_(voir_commentaires)	Not_found_yet
Cysteic_acid	Cysteic_acid	Amino_acids_peptides_and_analogues_	Alpha_amino_acids
S-Lactoylglutathione	S-Lactoylglutathione	Amino_acids_peptides_and_analogues_	Oligopeptides
5-Hydroxyindoleacetic_acid	5-Hydroxyindoleacetic_acid	Indolyl_carboxylic_acids_and_derivatives	Indole-3-acetic_acid_derivatives
Indole	Indole	Indoles_	Indoles
Indoleacetic_acid	Indoleacetic_acid	Indolyl_carboxylic_acids_and_derivatives	Indole-3-acetic_acid_derivatives
Indolepyruvate	Indolepyruvate	Indolyl_carboxylic_acids_and_derivatives	Indolyl_carboxylic_acids_and_derivatives
Indoxyl	Indoxyl	Hydroxyindoles_	Hydroxyindoles
Kynurenine	Kynurenine	Carbonyl_compounds	Alkyl-phenylketones
Quinolinic_acid	Quinolinic_acid	Pyridinecarboxylic_acids_and_derivatives	Pyridinecarboxylic_acids
N'-Formylkynurenine	N'-Formylkynurenine	Carbonyl_compounds	Alkyl-phenylketones
2-Aminobenzoic_acid	2-Aminobenzoic_acid	Benzoic_acids_and_derivatives	Aminobenzoic_acids
Picolinic_acid	Picolinic_acid	Pyridinecarboxylic_acids_and_derivatives	Pyridinecarboxylic_acids
gamma-Oxalocrotonate	gamma-Oxalocrotonate	Not_found_yet	Not_found_yet
5-Hydroxyindoleacetylglycine	5-Hydroxyindoleacetylglycine	Amino_acids_peptides_and_analogues_	N-acyl-alpha_amino_acids
Epinephrine	Epinephrine	Benzenediols	Catechols
Dopamine	Dopamine	Benzenediols	Catecholamines_and_derivatives
Serotonin	Serotonin	Tryptamines_and_derivatives	Serotonins
Ectoine	Ectoine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids_
3D-3.5/4-trihydroxycyclohexane-1.2-dione	3D-3,5/4-trihydroxycyclohexane-1,2-dione	Not_found_yet	Not_found_yet
glycerol-3-phosphate	glycerol-3-phosphate	Glycerophosphates	Glycerophosphates
O-Phosphoethanolamine	O-Phosphoethanolamine	Phosphate_esters_	Phosphoethanolamines
N-methylethanolamine_phosphate	N-methylethanolamine_phosphate	Phosphate_esters_	Alkyl_phosphates
Sphingosine_1-phosphate	Sphingosine_1-phosphate	Phosphosphingolipids	Phosphosphingolipids
Acetylcholine	Acetylcholine	Quaternary_ammonium_salts	Acyl_cholines
L-Carnitine	L-Carnitine	Quaternary_ammonium_salts	Carnitines
L-Acetylcarnitine	L-Acetylcarnitine	Fatty_acid_esters	Acyl_carnitines
Propionylcarnitine	Propionylcarnitine	Fatty_acid_esters	Acyl_carnitines
Butyrylcarnitine	Butyrylcarnitine	Fatty_acid_esters	Acyl_carnitines
3-Hydroxybutyrylcarnitine	3-Hydroxybutyrylcarnitine	Fatty_acid_esters	Acyl_carnitines
Tiglylcarnitine	Tiglylcarnitine	Fatty_acid_esters	Acyl_carnitines
2-Hydroxyisovalerylcarnitine	2-Hydroxyisovalerylcarnitine	Fatty_acid_esters	Acyl_carnitines
Hexanoylcarnitine	Hexanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Octanoylcarnitine	Octanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Octenoyl-L-carnitine	Octenoyl-L-carnitine	Medium-chain_keto_acids_and_derivatives_	Medium-chain_keto_acids_and_derivatives
Decenoylcarnitine	Decenoylcarnitine	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Dodecanoylcarnitine	Dodecanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
O-dodecenoyl-L-carnitine	O-dodecenoyl-L-carnitine
Tetradecanoylcarnitine	Tetradecanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Linoleoyl-CoA_	Linoleoyl-CoA_	Fatty_acyl_thioesters	Long-chain_fatty_acyl_CoAs
Caproic_acid	Caproic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Heptanoic_acid	Heptanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Caprylic_acid	Caprylic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Pelargonic_acid	Pelargonic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Capric_acid	Capric_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids_
Dodecanoic_acid	Dodecanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Myristic_acid	Myristic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Palmitic_acid	Palmitic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Stearic_acid	Stearic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Myristoleic_acid	Myristoleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Palmitoleic_acid	Palmitoleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Oleic_acid	Oleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Linoleic_acid	Linoleic_acid	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
alpha-Linolenic_acid	alpha-Linolenic_acid	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
Arachidonic_acid	Arachidonic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Stearidonic_acid	Stearidonic_acid	Lineolic_acids_and_derivatives_	Lineolic_acids_and_derivatives
Docosahexaenoic_acid	Docosahexaenoic_acid	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Dodecanedioic_acid	Dodecanedioic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Adrenic_acid	Adrenic_acid	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Eicosapentaenoic_acid	Eicosapentaenoic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Dihomo-gamma-linolenic_acid	Dihomo-gamma-linolenic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Docosapentaenoic_acid_(22n-3)	Docosapentaenoic_acid_(22n-3)	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Undecanoic_acid	Undecanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Deoxycholic_acid	Deoxycholic_acid	Bile_acids_alcohols_and_derivatives	Dihydroxy_bile_acids_alcohols_and_derivatives
Cholic_acid	Cholic_acid	Bile_acids_alcohols_and_derivatives	Trihydroxy_bile_acids_alcohols_and_derivatives
Chenodeoxyglycocholic_acid	Chenodeoxyglycocholic_acid	Bile_acids_alcohols_and_derivatives_	Glycinated_bile_acids_and_derivatives
Lithocholyltaurine	Lithocholyltaurine	Bile_acids_alcohols_and_derivatives	Taurinated_bile_acids_and_derivatives
6alpha-Glucuronosylhyodeoxycholate	6alpha-Glucuronosylhyodeoxycholate	Bile_acids_and_derivatives	C24_bile_acids_alcohols_and_derivatives
13-HODE	13-HODE	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
11(R)-HPETE	11(R)-HPETE	Eicosanoids_	Hydroperoxyeicosatetraenoic_acids
12.13-DHOME	12,13-DHOME	Fatty_acids_and_conjugates	Long-chain_fatty_acids
13-OxoODE	13-OxoODE	Lineolic_acids_and_derivatives_	Lineolic_acids_and_derivatives
Prostaglandin_A2	Prostaglandin_A2	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_D2	Prostaglandin_D2	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_F2a	Prostaglandin_F2a	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_D3	Prostaglandin_D3	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_G2	Prostaglandin_G2	Eicosanoids	Prostaglandins_and_related_compounds
Epiandrosterone	Epiandrosterone	Androstane_steroids_	Androgens_and_derivatives
Cortisol	Cortisol	Hydroxysteroids	21-hydroxysteroids
7alpha-Hydroxy-3-oxo-4-cholestenoate	7alpha-Hydroxy-3-oxo-4-cholestenoate	Bile_acids_alcohols_and_derivatives	Monohydroxy_bile_acids_alcohols_and_derivatives
11beta.17beta-Dihydroxy-4-androsten-3-one	11beta,17beta-Dihydroxy-4-androsten-3-one	Androstane_steroids	Androgens_and_derivatives
Pregnanediol	Pregnanediol	Pregnane_steroids	Gluco/mineralocorticoids_progestogins_and_derivatives
3beta-Hydroxypregn-5-en-20-one_sulfate	3beta-Hydroxypregn-5-en-20-one_sulfate	Sulfated_steroids	Sulfated_steroids
Pregnenolone	Pregnenolone	Pregnane_steroids	Gluco/mineralocorticoids_progestogins_and_derivatives
Pentobarbital	Pentobarbital	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
Biliverdin	Biliverdin	Bilirubins	Bilirubins
Bilirubin	Bilirubin	Bilirubins	Bilirubins

[Hugo_HAMMERLIN]

Hello,
I fixed my text file by doing multiple things :

• Removing spaces and replacing them by underscore, or removing when they were before tabulations
• Removed the last column, as I think it doesn’t help because it has a lot of missing values
• Corrected a line that was on multiple lines at the same time
• Verified if the lines had invisible characters with Notepad++

Still it gives me this error : Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 21 did not have 4 elements
Calls: readAndCheckF → read.table → scan

Here’s the text format of my file, I checked with multiple tools, and it says there are 4 columns, so I don’t know anymore…
Still, thank you for the assistance ! It helps me a lot !

Sample_ID	Variable_name	ClassFire_Sub_class	ClassFire_Parent_Level5
L-Alanine	L-Alanine	Amino_acids_peptides_and_analogues	Alanine_and_derivatives
L-Arginine	L-Arginine	Amino_acids_peptides_and_analogues 	L-alpha-amino_acids
L-Asparagine	L-Asparagine	Amino_acids_peptides_and_analogues	Asparagine_and_derivatives
L-aspartic_acid	L-aspartic_acid	Amino_acids_peptides_and_analogues	Aspartic_acid_and_derivatives
L-cysteine	L-cysteine	Amino_acids_peptides_and_analogues	Cysteine_and_derivatives
Glutamic_acid	Glutamic_acid	Amino_acids_peptides_and_analogues	Glutamic_acid_and_derivatives
Glutamine	Glutamine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Histidine	Histidine	Amino_acids_peptides_and_analogues	Histidine_and_derivatives
Isoleucine	Isoleucine	Amino_acids_peptides_and_analogues	Isoleucine_and_derivatives
Lysine	Lysine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Methionine	Methionine	_Amino_acids_peptides_and_analogues	Methionine_and_derivatives
Phenylalanine	Phenylalanine	Amino_acids_peptides_and_analogues	Phenylalanine_and_derivatives
Proline	Proline	Amino_acids_peptides_and_analogues	Proline_and_derivatives
Serine	Serine	Amino_acids_peptides_and_analogues	Serine_and_derivatives
L-Threonine	L-Threonine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
L-Tryptophan	L-Tryptophan	Indolyl_carboxylic_acids_and_derivatives	Indolyl_carboxylic_acids_and_derivatives
L-Tyrosine	L-Tyrosine	Amino_acids_peptides_and_analogues	Tyrosine_and_derivatives
L-Valine	L-Valine	Amino_acids_peptides_and_analogues	Valine_and_derivatives
L-Cystine	L-Cystine	Amino_acids_peptides_and_analogues	L-cysteine-S-conjugates
Adenosine_diphosphate	Adenosine_diphosphate	Purine_ribonucleotides	Purine_ribonucleoside_diphosphates
Deoxyadenosine_monophosphate	Deoxyadenosine_monophosphate	Purine_deoxyribonucleotides	Purine_2'-deoxyribonucleoside_monophosphates
cytidine	cytidine	Not_Available	Pyrimidine_nucleosides
Thymine	Thymine	Pyrimidines_and_pyrimidine_derivatives	Hydroxypyrimidines
Uridine_diphosphate	Uridine_diphosphate	Pyrimidine_ribonucleotides	Pyrimidine_ribonucleoside_diphosphates
Uracil	Uracil	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
IDP	IDP	Purine_ribonucleotides	Purine_ribonucleotides_diphosphates
Inosine	Inosine	Not_Available	Purine_nucleosides
Hypoxanthine	Hypoxanthine	Purines_and_purine_derivatives	Hypoxanthines
Xanthine	Xanthine	Purines_and_purine_derivatives	Xanthines
allantoic_acid	allantoic_acid	Amino_acids_peptides_and_analogues	N-carbamoyl-alpha_amino_acids
5-Hydroxyisourate	5-Hydroxyisourate	_Purines_and_purine_derivatives_	Xanthines
Cytidine_2'.3'-cyclic_phosphate	Cytidine_2',3'-cyclic_phosphate	Amino_acids_peptides_and_analogues	Peptides
Inosine_2'.3'-cyclic_phosphate	Inosine_2',3'-cyclic_phosphate	Cyclic_purine_nucleotides	2',3'-cyclic_purine_nucleotides
5.6-dihydrothymine	5,6-dihydrothymine	Pyrimidines_and_pyrimidine_derivatives_	Hydropyrimidines
Pyridoxamine_5'-phosphate	Pyridoxamine_5'-phosphate	Pyridoxamines	Pyridoxamine_5'-phosphates
Niacinamide	Niacinamide	Pyridinecarboxylic_acids_and_derivatives	Nicotinamides
Adenylsuccinic_acid	Adenylsuccinic_acid	Purine_ribonucleotides	Purine_ribonucleoside_monophosphates
NADPDP	Benzenediols	Catechols
NADD	Not_Available	(5'->5')-dinucleotides
Phosphate	Phosphate	Non-metal_phosphates	Non-metal_phosphates
diphosphate	diphosphate	Non-metal_pyrophosphates	Non-metal_pyrophosphates
D-Glucose	D-Glucose	Carbohydrates_and_carbohydrate_conjugates	Hexoses
glucose-1-phosphate	glucose-1-phosphate	Carbohydrates_and_carbohydrate_conjugates	Monosaccharide_phosphates
Glyceraldehyde_3-phosphate	Glyceraldehyde_3-phosphate	Carbohydrates_and_carbohydrate_conjugates	Glyceraldehyde-3-phosphates
2-Phosphoglycerate	2-Phosphoglycerate	Carbohydrates_and_carbohydrate_conjugates	Sugar_acids_and_derivatives
pyruvate	pyruvate	Keto_acids_and_derivatives	Alpha-keto_acids_and_derivatives
Lactic_acid	Lactic_acid	Alpha_hydroxy_acids_and_derivatives	Alpha_hydroxy_acids_and_derivatives
D-Maltose	D-Maltose	Carbohydrates_and_carbohydrate_conjugates	O-glycosyl_compounds
D-Ribose	D-Ribose	Carbohydrates_and_carbohydrate_conjugates	Pentoses
Rhamnose	Rhamnose	Carbohydrates_and_carbohydrate_conjugates	Hexoses
D-Arabitol	D-Arabitol	Carbohydrates_and_carbohydrate_conjugates	Sugar_alcohols
citrate	citrate	Tricarboxylic_acids_and_derivatives	Tricarboxylic_acids_and_derivatives
alpha-ketoglutarate	alpha-ketoglutarate	Gamma-keto_acids_and_derivatives	Gamma-keto_acids_and_derivatives
2-Keto-glutaramic_acid	2-Keto-glutaramic_acid	Short-chain_keto_acids_and_derivatives_	Short-chain_keto_acids_and_derivatives
succinate	succinate	Dicarboxylic_acids_and_derivatives	Dicarboxylic_acids_and_derivatives
fumarate	fumarate	Dicarboxylic_acids_and_derivatives 	Dicarboxylic_acids_and_derivatives 
Malate	Malate	Beta_hydroxy_acids_and_derivatives	Beta_hydroxy_acids_and_derivatives
Oxalacetic_acid	Oxalacetic_acid	Short-chain_keto_acids_and_derivatives	Short-chain_keto_acids_and_derivatives
2-Hydroxyglutarate	2-Hydroxyglutarate	Short-chain_hydroxy_acids_and_derivatives	Short-chain_hydroxy_acids_and_derivatives
ribose-1-phosphate	ribose-1-phosphate	Carbohydrates_and_carbohydrate_conjugates	Pentoses
Pyroglutamic_acid	Pyroglutamic_acid	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
ascorbate	ascorbate	Furanones	Butenolides
Dehydroascorbic_acid	Dehydroascorbic_acid	Gamma_butyrolactones	Gamma_butyrolactones
gamma-Glutamylcysteine	gamma-Glutamylcysteine	Amino_acids_peptides_and_analogues	N-acyl-alpha_amino_acids
Gamma-Glutamyl-Se-methylselenocysteine	Gamma-Glutamyl-Se-methylselenocysteine	Amino_acids_peptides_and_analogues	Dipeptides
gamma-Glutamylalanine	gamma-Glutamylalanine	Amino_acids_peptides_and_analogues	Dipeptides
Glutamylglutamine	Glutamylglutamine	Amino_acids_peptides_and_analogues	Dipeptides
Homocysteine	Homocysteine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Dimethylglycine	Dimethylglycine	Amino_acids_peptides_and_analogues_	Alpha_amino_acids
phosphoserine	phosphoserine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Ornithine	Ornithine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Citrulline	Citrulline	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Cadaverine	Cadaverine	Amines_	Monoalkylamines
Putrescine	Putrescine	Amines	Monoalkylamines
Spermidine	Spermidine	Amines	Dialkylamines
N-Acetylneuraminic_acid	N-Acetylneuraminic_acid	Carbohydrates_and_carbohydrate_conjugates	N-acylneuraminic_acids
N-Acetyl-glucosamine_1-phosphate	N-Acetyl-glucosamine_1-phosphate	Carbohydrates_and_carbohydrate_conjugates	N-acyl-alpha-hexosamines
?-D-xylan	?-D-xylan	Not_found_yet	Not_found_yet
Phosphocreatine	Phosphocreatine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
Creatine	Creatine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
Creatinine	Creatinine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
4-Acetamidobutanoic_acid	4-Acetamidobutanoic_acid	Amino_acids_peptides_and_analogues	Gamma_amino_acids_and_derivatives
N2-Acetylornithine	N2-Acetylornithine	Amino_acids_peptides_and_analogues	N-acyl-L-alpha-amino_acids
Guanidoacetic_acid	Guanidoacetic_acid	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
4-Hydroxyproline	4-Hydroxyproline	_Amino_acids_peptides_and_analogues	Proline_and_derivatives
N2-Succinyl-L-glutamic_acid_5-semialdehyde	N2-Succinyl-L-glutamic_acid_5-semialdehyde	Amino_acids_peptides_and_analogues	N-acyl-L-alpha-amino_acids
Pantothenol	Pantothenol	Fatty_amides	N-acyl_amines
Dihydrouracil	Dihydrouracil	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
Pantetheine	Pantetheine	Amino_acids_peptides_and_analogues	Beta_amino_acids_and_derivatives
Taurine	Taurine	Organosulfonic_acids_and_derivatives	Organosulfonic_acids
3-SULFOCATECHOL	3-SULFOCATECHOL	Not_found_yet_(voir_commentaires)	Not_found_yet
Cysteic_acid	Cysteic_acid	Amino_acids_peptides_and_analogues_	Alpha_amino_acids
S-Lactoylglutathione	S-Lactoylglutathione	Amino_acids_peptides_and_analogues_	Oligopeptides
5-Hydroxyindoleacetic_acid	5-Hydroxyindoleacetic_acid	Indolyl_carboxylic_acids_and_derivatives	Indole-3-acetic_acid_derivatives
Indole	Indole	Indoles_	Indoles
Indoleacetic_acid	Indoleacetic_acid	Indolyl_carboxylic_acids_and_derivatives	Indole-3-acetic_acid_derivatives
Indolepyruvate	Indolepyruvate	Indolyl_carboxylic_acids_and_derivatives	Indolyl_carboxylic_acids_and_derivatives
Indoxyl	Indoxyl	Hydroxyindoles_	Hydroxyindoles
Kynurenine	Kynurenine	Carbonyl_compounds	Alkyl-phenylketones
Quinolinic_acid	Quinolinic_acid	Pyridinecarboxylic_acids_and_derivatives	Pyridinecarboxylic_acids
N'-Formylkynurenine	N'-Formylkynurenine	Carbonyl_compounds	Alkyl-phenylketones
2-Aminobenzoic_acid	2-Aminobenzoic_acid	Benzoic_acids_and_derivatives	Aminobenzoic_acids
Picolinic_acid	Picolinic_acid	Pyridinecarboxylic_acids_and_derivatives	Pyridinecarboxylic_acids
gamma-Oxalocrotonate	gamma-Oxalocrotonate	Not_found_yet	Not_found_yet
5-Hydroxyindoleacetylglycine	5-Hydroxyindoleacetylglycine	Amino_acids_peptides_and_analogues_	N-acyl-alpha_amino_acids
Epinephrine	Epinephrine	Benzenediols	Catechols
Dopamine	Dopamine	Benzenediols	Catecholamines_and_derivatives
Serotonin	Serotonin	Tryptamines_and_derivatives	Serotonins
Ectoine	Ectoine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids_
3D-3.5/4-trihydroxycyclohexane-1.2-dione	3D-3,5/4-trihydroxycyclohexane-1,2-dione	Not_found_yet	Not_found_yet
glycerol-3-phosphate	glycerol-3-phosphate	Glycerophosphates	Glycerophosphates
O-Phosphoethanolamine	O-Phosphoethanolamine	Phosphate_esters_	Phosphoethanolamines
N-methylethanolamine_phosphate	N-methylethanolamine_phosphate	Phosphate_esters_	Alkyl_phosphates
Sphingosine_1-phosphate	Sphingosine_1-phosphate	Phosphosphingolipids	Phosphosphingolipids
Acetylcholine	Acetylcholine	Quaternary_ammonium_salts	Acyl_cholines
L-Carnitine	L-Carnitine	Quaternary_ammonium_salts	Carnitines
L-Acetylcarnitine	L-Acetylcarnitine	Fatty_acid_esters	Acyl_carnitines
Propionylcarnitine	Propionylcarnitine	Fatty_acid_esters	Acyl_carnitines
Butyrylcarnitine	Butyrylcarnitine	Fatty_acid_esters	Acyl_carnitines
3-Hydroxybutyrylcarnitine	3-Hydroxybutyrylcarnitine	Fatty_acid_esters	Acyl_carnitines
Tiglylcarnitine	Tiglylcarnitine	Fatty_acid_esters	Acyl_carnitines
2-Hydroxyisovalerylcarnitine	2-Hydroxyisovalerylcarnitine	Fatty_acid_esters	Acyl_carnitines
Hexanoylcarnitine	Hexanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Octanoylcarnitine	Octanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Octenoyl-L-carnitine	Octenoyl-L-carnitine	Medium-chain_keto_acids_and_derivatives_	Medium-chain_keto_acids_and_derivatives
Decenoylcarnitine	Decenoylcarnitine	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Dodecanoylcarnitine	Dodecanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
O-dodecenoyl-L-carnitine	O-dodecenoyl-L-carnitine
Tetradecanoylcarnitine	Tetradecanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Linoleoyl-CoA_	Linoleoyl-CoA_	Fatty_acyl_thioesters	Long-chain_fatty_acyl_CoAs
Caproic_acid	Caproic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Heptanoic_acid	Heptanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Caprylic_acid	Caprylic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Pelargonic_acid	Pelargonic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Capric_acid	Capric_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids_
Dodecanoic_acid	Dodecanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Myristic_acid	Myristic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Palmitic_acid	Palmitic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Stearic_acid	Stearic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Myristoleic_acid	Myristoleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Palmitoleic_acid	Palmitoleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Oleic_acid	Oleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Linoleic_acid	Linoleic_acid	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
alpha-Linolenic_acid	alpha-Linolenic_acid	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
Arachidonic_acid	Arachidonic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Stearidonic_acid	Stearidonic_acid	Lineolic_acids_and_derivatives_	Lineolic_acids_and_derivatives
Docosahexaenoic_acid	Docosahexaenoic_acid	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Dodecanedioic_acid	Dodecanedioic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Adrenic_acid	Adrenic_acid	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Eicosapentaenoic_acid	Eicosapentaenoic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Dihomo-gamma-linolenic_acid	Dihomo-gamma-linolenic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Docosapentaenoic_acid_(22n-3)	Docosapentaenoic_acid_(22n-3)	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Undecanoic_acid	Undecanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Deoxycholic_acid	Deoxycholic_acid	Bile_acids_alcohols_and_derivatives	Dihydroxy_bile_acids_alcohols_and_derivatives
Cholic_acid	Cholic_acid	Bile_acids_alcohols_and_derivatives	Trihydroxy_bile_acids_alcohols_and_derivatives
Chenodeoxyglycocholic_acid	Chenodeoxyglycocholic_acid	Bile_acids_alcohols_and_derivatives_	Glycinated_bile_acids_and_derivatives
Lithocholyltaurine	Lithocholyltaurine	Bile_acids_alcohols_and_derivatives	Taurinated_bile_acids_and_derivatives
6alpha-Glucuronosylhyodeoxycholate	6alpha-Glucuronosylhyodeoxycholate	Bile_acids_and_derivatives	C24_bile_acids_alcohols_and_derivatives
13-HODE	13-HODE	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
11(R)-HPETE	11(R)-HPETE	Eicosanoids_	Hydroperoxyeicosatetraenoic_acids
12.13-DHOME	12,13-DHOME	Fatty_acids_and_conjugates	Long-chain_fatty_acids
13-OxoODE	13-OxoODE	Lineolic_acids_and_derivatives_	Lineolic_acids_and_derivatives
Prostaglandin_A2	Prostaglandin_A2	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_D2	Prostaglandin_D2	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_F2a	Prostaglandin_F2a	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_D3	Prostaglandin_D3	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_G2	Prostaglandin_G2	Eicosanoids	Prostaglandins_and_related_compounds
Epiandrosterone	Epiandrosterone	Androstane_steroids_	Androgens_and_derivatives
Cortisol	Cortisol	Hydroxysteroids	21-hydroxysteroids
7alpha-Hydroxy-3-oxo-4-cholestenoate	7alpha-Hydroxy-3-oxo-4-cholestenoate	Bile_acids_alcohols_and_derivatives	Monohydroxy_bile_acids_alcohols_and_derivatives
11beta.17beta-Dihydroxy-4-androsten-3-one	11beta,17beta-Dihydroxy-4-androsten-3-one	Androstane_steroids	Androgens_and_derivatives
Pregnanediol	Pregnanediol	Pregnane_steroids	Gluco/mineralocorticoids_progestogins_and_derivatives
3beta-Hydroxypregn-5-en-20-one_sulfate	3beta-Hydroxypregn-5-en-20-one_sulfate	Sulfated_steroids	Sulfated_steroids
Pregnenolone	Pregnenolone	Pregnane_steroids	Gluco/mineralocorticoids_progestogins_and_derivatives
Pentobarbital	Pentobarbital	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
Biliverdin	Biliverdin	Bilirubins	Bilirubins
Bilirubin	Bilirubin	Bilirubins	Bilirubins

[Hugo_HAMMERLIN]

Hello,
I fixed my text file by doing multiple things :

• Removing spaces and replacing them by underscore, or removing when they were before tabulations
• Removed the last column, as I think it doesn’t help because it has a lot of missing values
• Corrected a line that was on multiple lines at the same time
• Verified if the lines had invisible characters with Notepad++

Still it gives me this error : Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 21 did not have 4 elements
Calls: readAndCheckF → read.table → scan

Here’s the text format of my file, I checked with multiple tools, and it says there are 4 columns, so I don’t know anymore…
Still, thank you for the assistance ! It helps me a lot !

Sample_ID Variable_name ClassFire_Sub_class ClassFire_Parent_Level5
L-Alanine L-Alanine Amino_acids_peptides_and_analogues Alanine_and_derivatives
L-Arginine L-Arginine Amino_acids_peptides_and_analogues L-alpha-amino_acids
L-Asparagine L-Asparagine Amino_acids_peptides_and_analogues Asparagine_and_derivatives
L-aspartic_acid L-aspartic_acid Amino_acids_peptides_and_analogues Aspartic_acid_and_derivatives
L-cysteine L-cysteine Amino_acids_peptides_and_analogues Cysteine_and_derivatives
Glutamic_acid Glutamic_acid Amino_acids_peptides_and_analogues Glutamic_acid_and_derivatives
Glutamine Glutamine Amino_acids_peptides_and_analogues L-alpha-amino_acids
Histidine Histidine Amino_acids_peptides_and_analogues Histidine_and_derivatives
Isoleucine Isoleucine Amino_acids_peptides_and_analogues Isoleucine_and_derivatives
Lysine Lysine Amino_acids_peptides_and_analogues L-alpha-amino_acids
Methionine Methionine Amino_acids_peptides_and_analogues Methionine_and_derivatives
Phenylalanine Phenylalanine Amino_acids_peptides_and_analogues Phenylalanine_and_derivatives
Proline Proline Amino_acids_peptides_and_analogues Proline_and_derivatives
Serine Serine Amino_acids_peptides_and_analogues Serine_and_derivatives
L-Threonine L-Threonine Amino_acids_peptides_and_analogues L-alpha-amino_acids
L-Tryptophan L-Tryptophan Indolyl_carboxylic_acids_and_derivatives Indolyl_carboxylic_acids_and_derivatives
L-Tyrosine L-Tyrosine Amino_acids_peptides_and_analogues Tyrosine_and_derivatives
L-Valine L-Valine Amino_acids_peptides_and_analogues Valine_and_derivatives
L-Cystine L-Cystine Amino_acids_peptides_and_analogues L-cysteine-S-conjugates
Adenosine_diphosphate Adenosine_diphosphate Purine_ribonucleotides Purine_ribonucleoside_diphosphates
Deoxyadenosine_monophosphate Deoxyadenosine_monophosphate Purine_deoxyribonucleotides Purine_2’-deoxyribonucleoside_monophosphates
cytidine cytidine Not_Available Pyrimidine_nucleosides
Thymine Thymine Pyrimidines_and_pyrimidine_derivatives Hydroxypyrimidines
Uridine_diphosphate Uridine_diphosphate Pyrimidine_ribonucleotides Pyrimidine_ribonucleoside_diphosphates
Uracil Uracil Pyrimidines_and_pyrimidine_derivatives Pyrimidones
IDP IDP Purine_ribonucleotides Purine_ribonucleotides_diphosphates
Inosine Inosine Not_Available Purine_nucleosides
Hypoxanthine Hypoxanthine Purines_and_purine_derivatives Hypoxanthines
Xanthine Xanthine Purines_and_purine_derivatives Xanthines
allantoic_acid allantoic_acid Amino_acids_peptides_and_analogues N-carbamoyl-alpha_amino_acids
5-Hydroxyisourate 5-Hydroxyisourate Purines_and_purine_derivatives Xanthines
Cytidine_2’.3’-cyclic_phosphate Cytidine_2’,3’-cyclic_phosphate Amino_acids_peptides_and_analogues Peptides
Inosine_2’.3’-cyclic_phosphate Inosine_2’,3’-cyclic_phosphate Cyclic_purine_nucleotides 2’,3’-cyclic_purine_nucleotides
5.6-dihydrothymine 5,6-dihydrothymine Pyrimidines_and_pyrimidine_derivatives Hydropyrimidines
Pyridoxamine_5’-phosphate Pyridoxamine_5’-phosphate Pyridoxamines Pyridoxamine_5’-phosphates
Niacinamide Niacinamide Pyridinecarboxylic_acids_and_derivatives Nicotinamides
Adenylsuccinic_acid Adenylsuccinic_acid Purine_ribonucleotides Purine_ribonucleoside_monophosphates
NADPDP Benzenediols Catechols
NADD Not_Available (5’->5’)-dinucleotides
Phosphate Phosphate Non-metal_phosphates Non-metal_phosphates
diphosphate diphosphate Non-metal_pyrophosphates Non-metal_pyrophosphates
D-Glucose D-Glucose Carbohydrates_and_carbohydrate_conjugates Hexoses
glucose-1-phosphate glucose-1-phosphate Carbohydrates_and_carbohydrate_conjugates Monosaccharide_phosphates
Glyceraldehyde_3-phosphate Glyceraldehyde_3-phosphate Carbohydrates_and_carbohydrate_conjugates Glyceraldehyde-3-phosphates
2-Phosphoglycerate 2-Phosphoglycerate Carbohydrates_and_carbohydrate_conjugates Sugar_acids_and_derivatives
pyruvate pyruvate Keto_acids_and_derivatives Alpha-keto_acids_and_derivatives
Lactic_acid Lactic_acid Alpha_hydroxy_acids_and_derivatives Alpha_hydroxy_acids_and_derivatives
D-Maltose D-Maltose Carbohydrates_and_carbohydrate_conjugates O-glycosyl_compounds
D-Ribose D-Ribose Carbohydrates_and_carbohydrate_conjugates Pentoses
Rhamnose Rhamnose Carbohydrates_and_carbohydrate_conjugates Hexoses
D-Arabitol D-Arabitol Carbohydrates_and_carbohydrate_conjugates Sugar_alcohols
citrate citrate Tricarboxylic_acids_and_derivatives Tricarboxylic_acids_and_derivatives
alpha-ketoglutarate alpha-ketoglutarate Gamma-keto_acids_and_derivatives Gamma-keto_acids_and_derivatives
2-Keto-glutaramic_acid 2-Keto-glutaramic_acid Short-chain_keto_acids_and_derivatives_ Short-chain_keto_acids_and_derivatives
succinate succinate Dicarboxylic_acids_and_derivatives Dicarboxylic_acids_and_derivatives
fumarate fumarate Dicarboxylic_acids_and_derivatives Dicarboxylic_acids_and_derivatives
Malate Malate Beta_hydroxy_acids_and_derivatives Beta_hydroxy_acids_and_derivatives
Oxalacetic_acid Oxalacetic_acid Short-chain_keto_acids_and_derivatives Short-chain_keto_acids_and_derivatives
2-Hydroxyglutarate 2-Hydroxyglutarate Short-chain_hydroxy_acids_and_derivatives Short-chain_hydroxy_acids_and_derivatives
ribose-1-phosphate ribose-1-phosphate Carbohydrates_and_carbohydrate_conjugates Pentoses
Pyroglutamic_acid Pyroglutamic_acid Amino_acids_peptides_and_analogues Alpha_amino_acids_and_derivatives
ascorbate ascorbate Furanones Butenolides
Dehydroascorbic_acid Dehydroascorbic_acid Gamma_butyrolactones Gamma_butyrolactones
gamma-Glutamylcysteine gamma-Glutamylcysteine Amino_acids_peptides_and_analogues N-acyl-alpha_amino_acids
Gamma-Glutamyl-Se-methylselenocysteine Gamma-Glutamyl-Se-methylselenocysteine Amino_acids_peptides_and_analogues Dipeptides
gamma-Glutamylalanine gamma-Glutamylalanine Amino_acids_peptides_and_analogues Dipeptides
Glutamylglutamine Glutamylglutamine Amino_acids_peptides_and_analogues Dipeptides
Homocysteine Homocysteine Amino_acids_peptides_and_analogues L-alpha-amino_acids
Dimethylglycine Dimethylglycine Amino_acids_peptides_and_analogues_ Alpha_amino_acids
phosphoserine phosphoserine Amino_acids_peptides_and_analogues L-alpha-amino_acids
Ornithine Ornithine Amino_acids_peptides_and_analogues L-alpha-amino_acids
Citrulline Citrulline Amino_acids_peptides_and_analogues L-alpha-amino_acids
Cadaverine Cadaverine Amines_ Monoalkylamines
Putrescine Putrescine Amines Monoalkylamines
Spermidine Spermidine Amines Dialkylamines
N-Acetylneuraminic_acid N-Acetylneuraminic_acid Carbohydrates_and_carbohydrate_conjugates N-acylneuraminic_acids
N-Acetyl-glucosamine_1-phosphate N-Acetyl-glucosamine_1-phosphate Carbohydrates_and_carbohydrate_conjugates N-acyl-alpha-hexosamines
?-D-xylan ?-D-xylan Not_found_yet Not_found_yet
Phosphocreatine Phosphocreatine Amino_acids_peptides_and_analogues Alpha_amino_acids_and_derivatives
Creatine Creatine Amino_acids_peptides_and_analogues Alpha_amino_acids_and_derivatives
Creatinine Creatinine Amino_acids_peptides_and_analogues Alpha_amino_acids_and_derivatives
4-Acetamidobutanoic_acid 4-Acetamidobutanoic_acid Amino_acids_peptides_and_analogues Gamma_amino_acids_and_derivatives
N2-Acetylornithine N2-Acetylornithine Amino_acids_peptides_and_analogues N-acyl-L-alpha-amino_acids
Guanidoacetic_acid Guanidoacetic_acid Amino_acids_peptides_and_analogues Alpha_amino_acids_and_derivatives
4-Hydroxyproline 4-Hydroxyproline Amino_acids_peptides_and_analogues Proline_and_derivatives
N2-Succinyl-L-glutamic_acid_5-semialdehyde N2-Succinyl-L-glutamic_acid_5-semialdehyde Amino_acids_peptides_and_analogues N-acyl-L-alpha-amino_acids
Pantothenol Pantothenol Fatty_amides N-acyl_amines
Dihydrouracil Dihydrouracil Pyrimidines_and_pyrimidine_derivatives Pyrimidones
Pantetheine Pantetheine Amino_acids_peptides_and_analogues Beta_amino_acids_and_derivatives
Taurine Taurine Organosulfonic_acids_and_derivatives Organosulfonic_acids
3-SULFOCATECHOL 3-SULFOCATECHOL Not_found_yet Not_found_yet
Cysteic_acid Cysteic_acid Amino_acids_peptides_and_analogues Alpha_amino_acids
S-Lactoylglutathione S-Lactoylglutathione Amino_acids_peptides_and_analogues_ Oligopeptides
5-Hydroxyindoleacetic_acid 5-Hydroxyindoleacetic_acid Indolyl_carboxylic_acids_and_derivatives Indole-3-acetic_acid_derivatives
Indole Indole Indoles_ Indoles
Indoleacetic_acid Indoleacetic_acid Indolyl_carboxylic_acids_and_derivatives Indole-3-acetic_acid_derivatives
Indolepyruvate Indolepyruvate Indolyl_carboxylic_acids_and_derivatives Indolyl_carboxylic_acids_and_derivatives
Indoxyl Indoxyl Hydroxyindoles_ Hydroxyindoles
Kynurenine Kynurenine Carbonyl_compounds Alkyl-phenylketones
Quinolinic_acid Quinolinic_acid Pyridinecarboxylic_acids_and_derivatives Pyridinecarboxylic_acids
N’-Formylkynurenine N’-Formylkynurenine Carbonyl_compounds Alkyl-phenylketones
2-Aminobenzoic_acid 2-Aminobenzoic_acid Benzoic_acids_and_derivatives Aminobenzoic_acids
Picolinic_acid Picolinic_acid Pyridinecarboxylic_acids_and_derivatives Pyridinecarboxylic_acids
gamma-Oxalocrotonate gamma-Oxalocrotonate Not_found_yet Not_found_yet
5-Hydroxyindoleacetylglycine 5-Hydroxyindoleacetylglycine Amino_acids_peptides_and_analogues_ N-acyl-alpha_amino_acids
Epinephrine Epinephrine Benzenediols Catechols
Dopamine Dopamine Benzenediols Catecholamines_and_derivatives
Serotonin Serotonin Tryptamines_and_derivatives Serotonins
Ectoine Ectoine Amino_acids_peptides_and_analogues L-alpha-amino_acids_
3D-3.5/4-trihydroxycyclohexane-1.2-dione 3D-3,5/4-trihydroxycyclohexane-1,2-dione Not_found_yet Not_found_yet
glycerol-3-phosphate glycerol-3-phosphate Glycerophosphates Glycerophosphates
O-Phosphoethanolamine O-Phosphoethanolamine Phosphate_esters_ Phosphoethanolamines
N-methylethanolamine_phosphate N-methylethanolamine_phosphate Phosphate_esters_ Alkyl_phosphates
Sphingosine_1-phosphate Sphingosine_1-phosphate Phosphosphingolipids Phosphosphingolipids
Acetylcholine Acetylcholine Quaternary_ammonium_salts Acyl_cholines
L-Carnitine L-Carnitine Quaternary_ammonium_salts Carnitines
L-Acetylcarnitine L-Acetylcarnitine Fatty_acid_esters Acyl_carnitines
Propionylcarnitine Propionylcarnitine Fatty_acid_esters Acyl_carnitines
Butyrylcarnitine Butyrylcarnitine Fatty_acid_esters Acyl_carnitines
3-Hydroxybutyrylcarnitine 3-Hydroxybutyrylcarnitine Fatty_acid_esters Acyl_carnitines
Tiglylcarnitine Tiglylcarnitine Fatty_acid_esters Acyl_carnitines
2-Hydroxyisovalerylcarnitine 2-Hydroxyisovalerylcarnitine Fatty_acid_esters Acyl_carnitines
Hexanoylcarnitine Hexanoylcarnitine Fatty_acid_esters Acyl_carnitines
Octanoylcarnitine Octanoylcarnitine Fatty_acid_esters Acyl_carnitines
Octenoyl-L-carnitine Octenoyl-L-carnitine Medium-chain_keto_acids_and_derivatives_ Medium-chain_keto_acids_and_derivatives
Decenoylcarnitine Decenoylcarnitine Fatty_acids_and_conjugates Long-chain_fatty_acids
Dodecanoylcarnitine Dodecanoylcarnitine Fatty_acid_esters Acyl_carnitines
O-dodecenoyl-L-carnitine O-dodecenoyl-L-carnitine
Tetradecanoylcarnitine Tetradecanoylcarnitine Fatty_acid_esters Acyl_carnitines
Linoleoyl-CoA_ Linoleoyl-CoA_ Fatty_acyl_thioesters Long-chain_fatty_acyl_CoAs
Caproic_acid Caproic_acid Fatty_acids_and_conjugates Medium-chain_fatty_acids
Heptanoic_acid Heptanoic_acid Fatty_acids_and_conjugates Medium-chain_fatty_acids
Caprylic_acid Caprylic_acid Fatty_acids_and_conjugates Medium-chain_fatty_acids
Pelargonic_acid Pelargonic_acid Fatty_acids_and_conjugates Medium-chain_fatty_acids
Capric_acid Capric_acid Fatty_acids_and_conjugates Medium-chain_fatty_acids_
Dodecanoic_acid Dodecanoic_acid Fatty_acids_and_conjugates Medium-chain_fatty_acids
Myristic_acid Myristic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Palmitic_acid Palmitic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Stearic_acid Stearic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Myristoleic_acid Myristoleic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Palmitoleic_acid Palmitoleic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Oleic_acid Oleic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Linoleic_acid Linoleic_acid Lineolic_acids_and_derivatives Lineolic_acids_and_derivatives
alpha-Linolenic_acid alpha-Linolenic_acid Lineolic_acids_and_derivatives Lineolic_acids_and_derivatives
Arachidonic_acid Arachidonic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Stearidonic_acid Stearidonic_acid Lineolic_acids_and_derivatives_ Lineolic_acids_and_derivatives
Docosahexaenoic_acid Docosahexaenoic_acid Fatty_acids_and_conjugates Very_long-chain_fatty_acids
Dodecanedioic_acid Dodecanedioic_acid Fatty_acids_and_conjugates Medium-chain_fatty_acids
Adrenic_acid Adrenic_acid Fatty_acids_and_conjugates Very_long-chain_fatty_acids
Eicosapentaenoic_acid Eicosapentaenoic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Dihomo-gamma-linolenic_acid Dihomo-gamma-linolenic_acid Fatty_acids_and_conjugates Long-chain_fatty_acids
Docosapentaenoic_acid_(22n-3) Docosapentaenoic_acid_(22n-3) Fatty_acids_and_conjugates Very_long-chain_fatty_acids
Undecanoic_acid Undecanoic_acid Fatty_acids_and_conjugates Medium-chain_fatty_acids
Deoxycholic_acid Deoxycholic_acid Bile_acids_alcohols_and_derivatives Dihydroxy_bile_acids_alcohols_and_derivatives
Cholic_acid Cholic_acid Bile_acids_alcohols_and_derivatives Trihydroxy_bile_acids_alcohols_and_derivatives
Chenodeoxyglycocholic_acid Chenodeoxyglycocholic_acid Bile_acids_alcohols_and_derivatives_ Glycinated_bile_acids_and_derivatives
Lithocholyltaurine Lithocholyltaurine Bile_acids_alcohols_and_derivatives Taurinated_bile_acids_and_derivatives
6alpha-Glucuronosylhyodeoxycholate 6alpha-Glucuronosylhyodeoxycholate Bile_acids_and_derivatives C24_bile_acids_alcohols_and_derivatives
13-HODE 13-HODE Lineolic_acids_and_derivatives Lineolic_acids_and_derivatives
11(R)-HPETE 11(R)-HPETE Eicosanoids_ Hydroperoxyeicosatetraenoic_acids
12.13-DHOME 12,13-DHOME Fatty_acids_and_conjugates Long-chain_fatty_acids
13-OxoODE 13-OxoODE Lineolic_acids_and_derivatives_ Lineolic_acids_and_derivatives
Prostaglandin_A2 Prostaglandin_A2 Eicosanoids Prostaglandins_and_related_compounds
Prostaglandin_D2 Prostaglandin_D2 Eicosanoids Prostaglandins_and_related_compounds
Prostaglandin_F2a Prostaglandin_F2a Eicosanoids Prostaglandins_and_related_compounds
Prostaglandin_D3 Prostaglandin_D3 Eicosanoids Prostaglandins_and_related_compounds
Prostaglandin_G2 Prostaglandin_G2 Eicosanoids Prostaglandins_and_related_compounds
Epiandrosterone Epiandrosterone Androstane_steroids_ Androgens_and_derivatives
Cortisol Cortisol Hydroxysteroids 21-hydroxysteroids
7alpha-Hydroxy-3-oxo-4-cholestenoate 7alpha-Hydroxy-3-oxo-4-cholestenoate Bile_acids_alcohols_and_derivatives Monohydroxy_bile_acids_alcohols_and_derivatives
11beta.17beta-Dihydroxy-4-androsten-3-one 11beta,17beta-Dihydroxy-4-androsten-3-one Androstane_steroids Androgens_and_derivatives
Pregnanediol Pregnanediol Pregnane_steroids Gluco/mineralocorticoids_progestogins_and_derivatives
3beta-Hydroxypregn-5-en-20-one_sulfate 3beta-Hydroxypregn-5-en-20-one_sulfate Sulfated_steroids Sulfated_steroids
Pregnenolone Pregnenolone Pregnane_steroids Gluco/mineralocorticoids_progestogins_and_derivatives
Pentobarbital Pentobarbital Pyrimidines_and_pyrimidine_derivatives Pyrimidones
Biliverdin Biliverdin Bilirubins Bilirubins
Bilirubin Bilirubin Bilirubins Bilirubins

[Hugo_HAMMERLIN]

Hello,
I fixed my text file by doing multiple things :

• Removing spaces and replacing them by underscore, or removing when they were before tabulations
• Removed the last column, as I think it doesn’t help because it has a lot of missing values
• Corrected a line that was on multiple lines at the same time
• Verified if the lines had invisible characters with Notepad++

Still it gives me this error : Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 21 did not have 4 elements
Calls: readAndCheckF → read.table → scan

I checked with multiple tools, and it says there are 4 columns, so I don’t know anymore…
Still, thank you for the assistance ! It helps me a lot !

Here is the link of my history https://metabolomics.usegalaxy.eu/u/hugo_hammerlin/h/univariate_test

[Hugo_HAMMERLIN]

Sample_ID	Variable_name	ClassFire_Sub_class	ClassFire_Parent_Level5
L-Alanine	L-Alanine	Amino_acids_peptides_and_analogues	Alanine_and_derivatives
L-Arginine	L-Arginine	Amino_acids_peptides_and_analogues 	L-alpha-amino_acids
L-Asparagine	L-Asparagine	Amino_acids_peptides_and_analogues	Asparagine_and_derivatives
L-aspartic_acid	L-aspartic_acid	Amino_acids_peptides_and_analogues	Aspartic_acid_and_derivatives
L-cysteine	L-cysteine	Amino_acids_peptides_and_analogues	Cysteine_and_derivatives
Glutamic_acid	Glutamic_acid	Amino_acids_peptides_and_analogues	Glutamic_acid_and_derivatives
Glutamine	Glutamine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Histidine	Histidine	Amino_acids_peptides_and_analogues	Histidine_and_derivatives
Isoleucine	Isoleucine	Amino_acids_peptides_and_analogues	Isoleucine_and_derivatives
Lysine	Lysine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Methionine	Methionine	_Amino_acids_peptides_and_analogues	Methionine_and_derivatives
Phenylalanine	Phenylalanine	Amino_acids_peptides_and_analogues	Phenylalanine_and_derivatives
Proline	Proline	Amino_acids_peptides_and_analogues	Proline_and_derivatives
Serine	Serine	Amino_acids_peptides_and_analogues	Serine_and_derivatives
L-Threonine	L-Threonine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
L-Tryptophan	L-Tryptophan	Indolyl_carboxylic_acids_and_derivatives	Indolyl_carboxylic_acids_and_derivatives
L-Tyrosine	L-Tyrosine	Amino_acids_peptides_and_analogues	Tyrosine_and_derivatives
L-Valine	L-Valine	Amino_acids_peptides_and_analogues	Valine_and_derivatives
L-Cystine	L-Cystine	Amino_acids_peptides_and_analogues	L-cysteine-S-conjugates
Adenosine_diphosphate	Adenosine_diphosphate	Purine_ribonucleotides	Purine_ribonucleoside_diphosphates
Deoxyadenosine_monophosphate	Deoxyadenosine_monophosphate	Purine_deoxyribonucleotides	Purine_2'-deoxyribonucleoside_monophosphates
cytidine	cytidine	Not_Available	Pyrimidine_nucleosides
Thymine	Thymine	Pyrimidines_and_pyrimidine_derivatives	Hydroxypyrimidines
Uridine_diphosphate	Uridine_diphosphate	Pyrimidine_ribonucleotides	Pyrimidine_ribonucleoside_diphosphates
Uracil	Uracil	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
IDP	IDP	Purine_ribonucleotides	Purine_ribonucleotides_diphosphates
Inosine	Inosine	Not_Available	Purine_nucleosides
Hypoxanthine	Hypoxanthine	Purines_and_purine_derivatives	Hypoxanthines
Xanthine	Xanthine	Purines_and_purine_derivatives	Xanthines
allantoic_acid	allantoic_acid	Amino_acids_peptides_and_analogues	N-carbamoyl-alpha_amino_acids
5-Hydroxyisourate	5-Hydroxyisourate	_Purines_and_purine_derivatives_	Xanthines
Cytidine_2'.3'-cyclic_phosphate	Cytidine_2',3'-cyclic_phosphate	Amino_acids_peptides_and_analogues	Peptides
Inosine_2'.3'-cyclic_phosphate	Inosine_2',3'-cyclic_phosphate	Cyclic_purine_nucleotides	2',3'-cyclic_purine_nucleotides
5.6-dihydrothymine	5,6-dihydrothymine	Pyrimidines_and_pyrimidine_derivatives_	Hydropyrimidines
Pyridoxamine_5'-phosphate	Pyridoxamine_5'-phosphate	Pyridoxamines	Pyridoxamine_5'-phosphates
Niacinamide	Niacinamide	Pyridinecarboxylic_acids_and_derivatives	Nicotinamides
Adenylsuccinic_acid	Adenylsuccinic_acid	Purine_ribonucleotides	Purine_ribonucleoside_monophosphates
NADPDP	Benzenediols	Catechols
NADD	Not_Available	(5'->5')-dinucleotides
Phosphate	Phosphate	Non-metal_phosphates	Non-metal_phosphates
diphosphate	diphosphate	Non-metal_pyrophosphates	Non-metal_pyrophosphates
D-Glucose	D-Glucose	Carbohydrates_and_carbohydrate_conjugates	Hexoses
glucose-1-phosphate	glucose-1-phosphate	Carbohydrates_and_carbohydrate_conjugates	Monosaccharide_phosphates
Glyceraldehyde_3-phosphate	Glyceraldehyde_3-phosphate	Carbohydrates_and_carbohydrate_conjugates	Glyceraldehyde-3-phosphates
2-Phosphoglycerate	2-Phosphoglycerate	Carbohydrates_and_carbohydrate_conjugates	Sugar_acids_and_derivatives
pyruvate	pyruvate	Keto_acids_and_derivatives	Alpha-keto_acids_and_derivatives
Lactic_acid	Lactic_acid	Alpha_hydroxy_acids_and_derivatives	Alpha_hydroxy_acids_and_derivatives
D-Maltose	D-Maltose	Carbohydrates_and_carbohydrate_conjugates	O-glycosyl_compounds
D-Ribose	D-Ribose	Carbohydrates_and_carbohydrate_conjugates	Pentoses
Rhamnose	Rhamnose	Carbohydrates_and_carbohydrate_conjugates	Hexoses
D-Arabitol	D-Arabitol	Carbohydrates_and_carbohydrate_conjugates	Sugar_alcohols
citrate	citrate	Tricarboxylic_acids_and_derivatives	Tricarboxylic_acids_and_derivatives
alpha-ketoglutarate	alpha-ketoglutarate	Gamma-keto_acids_and_derivatives	Gamma-keto_acids_and_derivatives
2-Keto-glutaramic_acid	2-Keto-glutaramic_acid	Short-chain_keto_acids_and_derivatives_	Short-chain_keto_acids_and_derivatives
succinate	succinate	Dicarboxylic_acids_and_derivatives	Dicarboxylic_acids_and_derivatives
fumarate	fumarate	Dicarboxylic_acids_and_derivatives 	Dicarboxylic_acids_and_derivatives 
Malate	Malate	Beta_hydroxy_acids_and_derivatives	Beta_hydroxy_acids_and_derivatives
Oxalacetic_acid	Oxalacetic_acid	Short-chain_keto_acids_and_derivatives	Short-chain_keto_acids_and_derivatives
2-Hydroxyglutarate	2-Hydroxyglutarate	Short-chain_hydroxy_acids_and_derivatives	Short-chain_hydroxy_acids_and_derivatives
ribose-1-phosphate	ribose-1-phosphate	Carbohydrates_and_carbohydrate_conjugates	Pentoses
Pyroglutamic_acid	Pyroglutamic_acid	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
ascorbate	ascorbate	Furanones	Butenolides
Dehydroascorbic_acid	Dehydroascorbic_acid	Gamma_butyrolactones	Gamma_butyrolactones
gamma-Glutamylcysteine	gamma-Glutamylcysteine	Amino_acids_peptides_and_analogues	N-acyl-alpha_amino_acids
Gamma-Glutamyl-Se-methylselenocysteine	Gamma-Glutamyl-Se-methylselenocysteine	Amino_acids_peptides_and_analogues	Dipeptides
gamma-Glutamylalanine	gamma-Glutamylalanine	Amino_acids_peptides_and_analogues	Dipeptides
Glutamylglutamine	Glutamylglutamine	Amino_acids_peptides_and_analogues	Dipeptides
Homocysteine	Homocysteine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Dimethylglycine	Dimethylglycine	Amino_acids_peptides_and_analogues_	Alpha_amino_acids
phosphoserine	phosphoserine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Ornithine	Ornithine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Citrulline	Citrulline	Amino_acids_peptides_and_analogues	L-alpha-amino_acids
Cadaverine	Cadaverine	Amines_	Monoalkylamines
Putrescine	Putrescine	Amines	Monoalkylamines
Spermidine	Spermidine	Amines	Dialkylamines
N-Acetylneuraminic_acid	N-Acetylneuraminic_acid	Carbohydrates_and_carbohydrate_conjugates	N-acylneuraminic_acids
N-Acetyl-glucosamine_1-phosphate	N-Acetyl-glucosamine_1-phosphate	Carbohydrates_and_carbohydrate_conjugates	N-acyl-alpha-hexosamines
?-D-xylan	?-D-xylan	Not_found_yet	Not_found_yet
Phosphocreatine	Phosphocreatine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
Creatine	Creatine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
Creatinine	Creatinine	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
4-Acetamidobutanoic_acid	4-Acetamidobutanoic_acid	Amino_acids_peptides_and_analogues	Gamma_amino_acids_and_derivatives
N2-Acetylornithine	N2-Acetylornithine	Amino_acids_peptides_and_analogues	N-acyl-L-alpha-amino_acids
Guanidoacetic_acid	Guanidoacetic_acid	Amino_acids_peptides_and_analogues	Alpha_amino_acids_and_derivatives
4-Hydroxyproline	4-Hydroxyproline	_Amino_acids_peptides_and_analogues	Proline_and_derivatives
N2-Succinyl-L-glutamic_acid_5-semialdehyde	N2-Succinyl-L-glutamic_acid_5-semialdehyde	Amino_acids_peptides_and_analogues	N-acyl-L-alpha-amino_acids
Pantothenol	Pantothenol	Fatty_amides	N-acyl_amines
Dihydrouracil	Dihydrouracil	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
Pantetheine	Pantetheine	Amino_acids_peptides_and_analogues	Beta_amino_acids_and_derivatives
Taurine	Taurine	Organosulfonic_acids_and_derivatives	Organosulfonic_acids
3-SULFOCATECHOL	3-SULFOCATECHOL	Not_found_yet	Not_found_yet
Cysteic_acid	Cysteic_acid	Amino_acids_peptides_and_analogues_	Alpha_amino_acids
S-Lactoylglutathione	S-Lactoylglutathione	Amino_acids_peptides_and_analogues_	Oligopeptides
5-Hydroxyindoleacetic_acid	5-Hydroxyindoleacetic_acid	Indolyl_carboxylic_acids_and_derivatives	Indole-3-acetic_acid_derivatives
Indole	Indole	Indoles_	Indoles
Indoleacetic_acid	Indoleacetic_acid	Indolyl_carboxylic_acids_and_derivatives	Indole-3-acetic_acid_derivatives
Indolepyruvate	Indolepyruvate	Indolyl_carboxylic_acids_and_derivatives	Indolyl_carboxylic_acids_and_derivatives
Indoxyl	Indoxyl	Hydroxyindoles_	Hydroxyindoles
Kynurenine	Kynurenine	Carbonyl_compounds	Alkyl-phenylketones
Quinolinic_acid	Quinolinic_acid	Pyridinecarboxylic_acids_and_derivatives	Pyridinecarboxylic_acids
N'-Formylkynurenine	N'-Formylkynurenine	Carbonyl_compounds	Alkyl-phenylketones
2-Aminobenzoic_acid	2-Aminobenzoic_acid	Benzoic_acids_and_derivatives	Aminobenzoic_acids
Picolinic_acid	Picolinic_acid	Pyridinecarboxylic_acids_and_derivatives	Pyridinecarboxylic_acids
gamma-Oxalocrotonate	gamma-Oxalocrotonate	Not_found_yet	Not_found_yet
5-Hydroxyindoleacetylglycine	5-Hydroxyindoleacetylglycine	Amino_acids_peptides_and_analogues_	N-acyl-alpha_amino_acids
Epinephrine	Epinephrine	Benzenediols	Catechols
Dopamine	Dopamine	Benzenediols	Catecholamines_and_derivatives
Serotonin	Serotonin	Tryptamines_and_derivatives	Serotonins
Ectoine	Ectoine	Amino_acids_peptides_and_analogues	L-alpha-amino_acids_
3D-3.5/4-trihydroxycyclohexane-1.2-dione	3D-3,5/4-trihydroxycyclohexane-1,2-dione	Not_found_yet	Not_found_yet
glycerol-3-phosphate	glycerol-3-phosphate	Glycerophosphates	Glycerophosphates
O-Phosphoethanolamine	O-Phosphoethanolamine	Phosphate_esters_	Phosphoethanolamines
N-methylethanolamine_phosphate	N-methylethanolamine_phosphate	Phosphate_esters_	Alkyl_phosphates
Sphingosine_1-phosphate	Sphingosine_1-phosphate	Phosphosphingolipids	Phosphosphingolipids
Acetylcholine	Acetylcholine	Quaternary_ammonium_salts	Acyl_cholines
L-Carnitine	L-Carnitine	Quaternary_ammonium_salts	Carnitines
L-Acetylcarnitine	L-Acetylcarnitine	Fatty_acid_esters	Acyl_carnitines
Propionylcarnitine	Propionylcarnitine	Fatty_acid_esters	Acyl_carnitines
Butyrylcarnitine	Butyrylcarnitine	Fatty_acid_esters	Acyl_carnitines
3-Hydroxybutyrylcarnitine	3-Hydroxybutyrylcarnitine	Fatty_acid_esters	Acyl_carnitines
Tiglylcarnitine	Tiglylcarnitine	Fatty_acid_esters	Acyl_carnitines
2-Hydroxyisovalerylcarnitine	2-Hydroxyisovalerylcarnitine	Fatty_acid_esters	Acyl_carnitines
Hexanoylcarnitine	Hexanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Octanoylcarnitine	Octanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Octenoyl-L-carnitine	Octenoyl-L-carnitine	Medium-chain_keto_acids_and_derivatives_	Medium-chain_keto_acids_and_derivatives
Decenoylcarnitine	Decenoylcarnitine	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Dodecanoylcarnitine	Dodecanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
O-dodecenoyl-L-carnitine	O-dodecenoyl-L-carnitine
Tetradecanoylcarnitine	Tetradecanoylcarnitine	Fatty_acid_esters	Acyl_carnitines
Linoleoyl-CoA_	Linoleoyl-CoA_	Fatty_acyl_thioesters	Long-chain_fatty_acyl_CoAs
Caproic_acid	Caproic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Heptanoic_acid	Heptanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Caprylic_acid	Caprylic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Pelargonic_acid	Pelargonic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Capric_acid	Capric_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids_
Dodecanoic_acid	Dodecanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Myristic_acid	Myristic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Palmitic_acid	Palmitic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Stearic_acid	Stearic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Myristoleic_acid	Myristoleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Palmitoleic_acid	Palmitoleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Oleic_acid	Oleic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Linoleic_acid	Linoleic_acid	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
alpha-Linolenic_acid	alpha-Linolenic_acid	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
Arachidonic_acid	Arachidonic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Stearidonic_acid	Stearidonic_acid	Lineolic_acids_and_derivatives_	Lineolic_acids_and_derivatives
Docosahexaenoic_acid	Docosahexaenoic_acid	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Dodecanedioic_acid	Dodecanedioic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Adrenic_acid	Adrenic_acid	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Eicosapentaenoic_acid	Eicosapentaenoic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Dihomo-gamma-linolenic_acid	Dihomo-gamma-linolenic_acid	Fatty_acids_and_conjugates	Long-chain_fatty_acids
Docosapentaenoic_acid_(22n-3)	Docosapentaenoic_acid_(22n-3)	Fatty_acids_and_conjugates	Very_long-chain_fatty_acids
Undecanoic_acid	Undecanoic_acid	Fatty_acids_and_conjugates	Medium-chain_fatty_acids
Deoxycholic_acid	Deoxycholic_acid	Bile_acids_alcohols_and_derivatives	Dihydroxy_bile_acids_alcohols_and_derivatives
Cholic_acid	Cholic_acid	Bile_acids_alcohols_and_derivatives	Trihydroxy_bile_acids_alcohols_and_derivatives
Chenodeoxyglycocholic_acid	Chenodeoxyglycocholic_acid	Bile_acids_alcohols_and_derivatives_	Glycinated_bile_acids_and_derivatives
Lithocholyltaurine	Lithocholyltaurine	Bile_acids_alcohols_and_derivatives	Taurinated_bile_acids_and_derivatives
6alpha-Glucuronosylhyodeoxycholate	6alpha-Glucuronosylhyodeoxycholate	Bile_acids_and_derivatives	C24_bile_acids_alcohols_and_derivatives
13-HODE	13-HODE	Lineolic_acids_and_derivatives	Lineolic_acids_and_derivatives
11(R)-HPETE	11(R)-HPETE	Eicosanoids_	Hydroperoxyeicosatetraenoic_acids
12.13-DHOME	12,13-DHOME	Fatty_acids_and_conjugates	Long-chain_fatty_acids
13-OxoODE	13-OxoODE	Lineolic_acids_and_derivatives_	Lineolic_acids_and_derivatives
Prostaglandin_A2	Prostaglandin_A2	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_D2	Prostaglandin_D2	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_F2a	Prostaglandin_F2a	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_D3	Prostaglandin_D3	Eicosanoids	Prostaglandins_and_related_compounds
Prostaglandin_G2	Prostaglandin_G2	Eicosanoids	Prostaglandins_and_related_compounds
Epiandrosterone	Epiandrosterone	Androstane_steroids_	Androgens_and_derivatives
Cortisol	Cortisol	Hydroxysteroids	21-hydroxysteroids
7alpha-Hydroxy-3-oxo-4-cholestenoate	7alpha-Hydroxy-3-oxo-4-cholestenoate	Bile_acids_alcohols_and_derivatives	Monohydroxy_bile_acids_alcohols_and_derivatives
11beta.17beta-Dihydroxy-4-androsten-3-one	11beta,17beta-Dihydroxy-4-androsten-3-one	Androstane_steroids	Androgens_and_derivatives
Pregnanediol	Pregnanediol	Pregnane_steroids	Gluco/mineralocorticoids_progestogins_and_derivatives
3beta-Hydroxypregn-5-en-20-one_sulfate	3beta-Hydroxypregn-5-en-20-one_sulfate	Sulfated_steroids	Sulfated_steroids
Pregnenolone	Pregnenolone	Pregnane_steroids	Gluco/mineralocorticoids_progestogins_and_derivatives
Pentobarbital	Pentobarbital	Pyrimidines_and_pyrimidine_derivatives	Pyrimidones
Biliverdin	Biliverdin	Bilirubins	Bilirubins
Bilirubin	Bilirubin	Bilirubins	Bilirubins

[jennaj]

Ok, thanks for sharing back some file details @Hugo_HAMMERLIN

(and next time, just post once. a moderator will approve it once here in their time zone)

It is great that you resolved any whitespace issues. From here, you can tackle special characters. I could have mentioned this as another item to the list above

6. Check for special characters

   Letters and numbers might be Ok, or just letters, or just numbers.

   Underscore versus dash characters being Ok or not depends on the tool.

   Starting with a number might be Ok, but might not be.

   Including any other characters is usually not allowed unless that term value is something like a description, and those might need to be quoted.

Looking at the manual, this is an R tool. That means

only letters, numbers, and underscores, and not starting with a number, for any term that is not just a description, if spaces are included they must not be key terms matched across files and they should be quoted.

Now, you might be able to “quote” terms to allow for other characters, I’m not sure if that is allowed by this specific tool yet.

I created a test history to compare to here. Maybe try inspecting those formats to see what is exactly different in your files as you work through this? You could also refer to the tool guide.

• https://usegalaxy.eu/u/jenj/h/test-check-format
• See → GitHub - workflow4metabolomics/checkformat: Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files. There is a link to an example history at a different public Galaxy server, but you can have an account there too, or just view that history.

What to do – one or both of these are usual paths depending on which examples you find. You can use one of the Replace tools for this.

• Add in quoting. Do this by adding a " character to the start of every line, the end of every line, and then replace every tab with a “tab” three characters. This will add in a " around each term.

• Try substituting or maybe better, just removing, all the other special characters instead.

Hope this helps!