wrong number of fields

[liushuqing506]

Prerequisites

• [x] make sure you're are using the latest version by csvtk version
• [x] read the usage

Describe your issue

taxonkit 联合 csvtk 使用中，使用了-I参数，但是结果依然出现[ERRO] record on line 25397: wrong number of fields

cat db_supplement_sta_addClassification_genomedata_nt.taxid.list | taxonkit lineage | taxonkit reformat -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -F -P | csvtk cut -t -f -2 | csvtk add-header -I -t -n taxid,kindom,phylum,class,order,family,genus,species > db_supplement_sta_addClassification_genomedata_nt.taxon.tsv

Thank you

I'm grateful to users who have greatly helped to report bugs and suggested new features.

I may respond to issues or fix bugs quickly, but I usually implement new features periodically (two or more weeks).

[shenwei356]

不建议用 taxonkit lineage | taxonkit reformat 了，建议直接用 taxonkit reformat -I 1 （指定taxid所在列）

请用awk把 25397行打印出来看看。

[liushuqing506]

我把-I参数填在csvtk cut后面了，不报错了。

[liushuqing506]

我试用了taxonkit reformat -I 1 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -F -P，但是报错 [ERRO] number of fields (7) and new colnames (8) do not match

[liushuqing506]

25397行的taxid可能是因为taxonkit没有分类结果，是空的

[shenwei356]

你给个例子吧，把25397行和前后的发来看看

[shenwei356]

$ cat db_supplement_sta_addClassification_genomedata_nt.taxid.list 
9606
12345678
452

cat db_supplement_sta_addClassification_genomedata_nt.taxid.list \
    | taxonkit reformat -I 1 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -F -P \
    | csvtk add-header -I -t -n taxid,kindom,phylum,class,order,family,genus,species

taxid   kindom  phylum  class   order   family  genus   species
9606    k__Eukaryota    p__Chordata     c__Mammalia     o__Primates     f__Hominidae    g__Homo s__Homo sapiens
12345678
452     k__Bacteria     p__Pseudomonadota       c__Gammaproteobacteria  o__Legionellales        f__Legionellaceae       g__Legionella   s__Legionella spiritensis

甚至不需要用csvtk

echo -e "taxid\tkindom\tphylum\tclass\torder\tfamily\tgenus\tspecies";
cat db_supplement_sta_addClassification_genomedata_nt.taxid.list \
    | taxonkit reformat -I 1 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -F -P

[liushuqing506]

谢谢，沈老师

------------------ 原始邮件 ------------------ 发件人: "Wei @.>; 发送时间: 2023年6月13日(星期二) 上午10:39 收件人: @.>; 抄送: @.>; @.>; 主题: Re: [shenwei356/csvtk] wrong number of fields (Issue #229)

$ cat db_supplement_sta_addClassification_genomedata_nt.taxid.list 9606 12345678 452 cat db_supplement_sta_addClassification_genomedata_nt.taxid.list \ | taxonkit reformat -I 1 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -F -P \ | csvtk add-header -I -t -n taxid,kindom,phylum,class,order,family,genus,species taxid kindom phylum class order family genus species 9606 kEukaryota pChordata cMammalia oPrimates fHominidae gHomo sHomo sapiens 12345678 452 kBacteria pPseudomonadota cGammaproteobacteria oLegionellales fLegionellaceae gLegionella sLegionella spiritensis
甚至不需要用csvtk echo -e "taxid\tkindom\tphylum\tclass\torder\tfamily\tgenus\tspecies"; cat db_supplement_sta_addClassification_genomedata_nt.taxid.list \ | taxonkit reformat -I 1 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -F -P
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