<p>The reason is (likely) that plink is expecting a space separated file for the <code>--update-name</code> argument:</p>
<pre><code>--update-name &lt;filename&gt; [new ID col. number] [old ID col.] [skip]
</code></pre>
<p>You've given it a comma-separated file, so it thinks there is only one column, hence the error. You also don't want column names.</p>
<p>Change the sep by:</p>
<pre><code>sed 's/,/ /g' updated_ref.csv &gt; updated_ref.txt
</code></pre>
<p>Or, edit the file in place, and keep a backup of the original named <code>updated_ref.csv.bak</code> :</p>
<pre><code>sed -i.bak 's/,/ /g' updated_ref.csv &gt; updated_ref.txt
</code></pre>

CC BY-SA 4.0
2021-06-10T13:01:11.080Z
Do you mean cat updated_ref.csv | sed -i 's/,/ /g' > updated_ref.txt 
 according to my data and it will convert my .csv into .txt?
Aryh
CC BY-SA 4.0
2021-06-10T13:03:43.197Z
See update to my post
user438383
CC BY-SA 4.0
2021-06-10T12:49:39.123Z
2021-06-10T13:19:48.300Z
2021-06-10T13:19:48.300Z
user438383
<p>I am trying to update my rsIDs in .bim file by using --update-name flag in plink but getting this error message. what could be the reason of it?</p>
<pre><code>plink --bfile updated_ff  --update-name updated_ref.csv --make-bed --out test_updatedrs

PLINK v1.90b6.21 64-bit (19 Oct 2020)
Options in effect:
  --bfile updated_ff
  --make-bed
  --out test_updatedrs
  --update-name updated_ref.csv

Hostname: login1
Working directory: /gpfs/home/bsc08/bsc08856/phs001273_dbgap
Start time: Thu Jun 10 14:23:44 2021

Random number seed: 1623327824
96310 MB RAM detected; reserving 48155 MB for main workspace.
Allocated 15236 MB successfully, after larger attempt(s) failed.
Error: Line 1 of updated_ref.csv has fewer tokens than expected.
</code></pre>
<p>My updated_ref.csv file looks like this</p>
<pre><code>Name,chrpos
rs3793692,chr10_100008436
rs1983865,chr10_100016339
newrs150271620,chr10_100017402
rs10736126,chr10_100025924
chr10_100044928_A_G,chr10_100044928
rs7905091,chr10_100046078
rs6584182,chr10_100055644
chr10_100058710_C_T,chr10_100058710
rs4360594,chr10_10007547
rs927739,chr10_100077732
rs4917817,chr10_100085888
</code></pre>
<p>while my .bim looks like this</p>
<pre><code>1 rs3094315 0 752566 G A
1 rs3131972 0 752721 A G
1 chr1770377 0 770377 T A
1 rs11240777 0 798959 A G
1 chr1834753 0 834753 C G
1 rs72890788 0 836924 A G
1 rs4970383 0 838555 A C
1 chr1840753 0 840753 G A

1 rs4475691 0 846808 A G
</code></pre>

<plink>
Error: "fewer tokens than expected" while using --update-name flag in plink
# Error: "fewer tokens than expected" while using --update-name flag in plink

(Asked by: username_0 on 2021-06-10)

I am trying to update my rsIDs in .bim file by using --update-name flag in plink but getting this error message. what could be the reason of it?
plink --bfile updated_ff  --update-name updated_ref.csv --make-bed --out test_updatedrs

PLINK v1.90b6.21 64-bit (19 Oct 2020)
Options in effect:
  --bfile updated_ff
  --make-bed
  --out test_updatedrs
  --update-name updated_ref.csv

Hostname: login1
Working directory: /gpfs/home/bsc08/bsc08856/phs001273_dbgap
Start time: Thu Jun 10 14:23:44 2021

Random number seed: 1623327824
96310 MB RAM detected; reserving 48155 MB for main workspace.
Allocated 15236 MB successfully, after larger attempt(s) failed.
Error: Line 1 of updated_ref.csv has fewer tokens than expected.

My updated_ref.csv file looks like this
Name,chrpos
rs3793692,chr10_100008436
rs1983865,chr10_100016339
newrs150271620,chr10_100017402
rs10736126,chr10_100025924
chr10_100044928_A_G,chr10_100044928
rs7905091,chr10_100046078
rs6584182,chr10_100055644
chr10_100058710_C_T,chr10_100058710
rs4360594,chr10_10007547
rs927739,chr10_100077732
rs4917817,chr10_100085888

while my .bim looks like this
1 rs3094315 0 752566 G A
1 rs3131972 0 752721 A G
1 chr1770377 0 770377 T A
1 rs11240777 0 798959 A G
1 chr1834753 0 834753 C G
1 rs72890788 0 836924 A G
1 rs4970383 0 838555 A C
1 chr1840753 0 840753 G A

1 rs4475691 0 846808 A G

**Tags:** plink

---

## 1 answers

### Answer by username_1 on 2021-06-10. Score: 2 | Accepted answer

The reason is (likely) that plink is expecting a space separated file for the --update-name argument:
--update-name  [new ID col. number] [old ID col.] [skip]

You've given it a comma-separated file, so it thinks there is only one column, hence the error. You also don't want column names.
Change the sep by:
sed 's/,/ /g' updated_ref.csv > updated_ref.txt

Or, edit the file in place, and keep a backup of the original named updated_ref.csv.bak :
sed -i.bak 's/,/ /g' updated_ref.csv > updated_ref.txt

> **Comments:**
> **username_0**: Do you mean cat updated_ref.csv | sed -i 's/,/ /g' > updated_ref.txt   according to my data and it will convert my .csv into .txt?  
> **username_1**: See update to my post  

---

