# Error during pcr.seqs step: Error in reading your fastafile, at position -1. Blank name **URL:** \ **Category:** mothur bugs\ **Created:** [September 25, 2025, 1:04pm UTC](https://forum.mothur.org/t/error-during-pcr-seqs-step-error-in-reading-your-fastafile-at-position-1-blank-name/22364 "2025-09-25T13:04:52Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![sbelz](https://avatars.discourse-cdn.com/v4/letter/s/94ad74/32.png) [@sbelz](https://forum.mothur.org/u/sbelz)\ **Post date:** [September 25, 2025, 1:04pm UTC](https://forum.mothur.org/t/error-during-pcr-seqs-step-error-in-reading-your-fastafile-at-position-1-blank-name/22364/1 "2025-09-25T13:04:52Z")
Hello all! I am rather new to Mothur and am looking to get some help resolving this issue. I’m using Mothur v1.48.3 and was running the pcr.seqs command: _pcr.seqs(fasta= FILENAME.trim.contigs.fasta, count= FILENAME.contigs.count\_table, oligos=oligos16.txt, pdiffs=2, rdiffs=2)_ and it ran for a while (several hours at least), but when I checked it this morning the last few lines of text in mothur.exe read as follows: _[..]_ _1727828 888427 Error in reading your fastafile, at position -1. Blank name. 496418 Error in reading your fastafile, at position -1. Blank name. 1446998 1847098_ _mothur \>_ There were no output files listed so I am inclined to believe that along with the errors, the command didn’t actually compete - though I may be wrong. If someone could offer some guidance that would be greatly appreciated. ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [September 29, 2025, 1:39pm UTC](https://forum.mothur.org/t/error-during-pcr-seqs-step-error-in-reading-your-fastafile-at-position-1-blank-name/22364/2 "2025-09-29T13:39:12Z")
Hey - Welcome to mothur! Can you post the commands you ran upstream of pcr.seqs? Also, what operating system are you running mothur on? Thanks, Pat ---
**Author:** ![sbelz](https://avatars.discourse-cdn.com/v4/letter/s/94ad74/32.png) [@sbelz](https://forum.mothur.org/u/sbelz)\ **Post date:** [September 30, 2025, 1:01pm UTC](https://forum.mothur.org/t/error-during-pcr-seqs-step-error-in-reading-your-fastafile-at-position-1-blank-name/22364/3 "2025-09-30T13:01:24Z")
Thank you for the reply! I am running Mothur on Windows. Here are the commands I ran leading up to this: **mothur \> make.file(inputdir=mme\_wd, type=fastq, prefix=mme\_wd\_fasta)** Output File Names: mme\_wd\mme\_wd\_fasta.files **mothur \> make.contigs(file= mme\_wd\_fasta.files, processors=8)** Output File Names: mme\_wd\mme\_wd\_fasta.trim.contigs.fasta mme\_wd\mme\_wd\_fasta.scrap.contigs.fasta mme\_wd\mme\_wd\_fasta.contigs\_report mme\_wd\mme\_wd\_fasta.contigs.count\_table **mothur \> summary.seqs(fasta= mme\_wd\_fasta.trim.contigs.fasta)** Output File Names: mme\_wd\_fasta.trim.contigs.summary Created a .txt file (in this case using notepad) named oligos16, copy/pasted the primer sequences listed below, and saved into the mme\_wd file. _forward GTGYCAGCMGCCGCGGTAA_ _reverse GGACTACNVGGGTWTCTAAT_ **mothur \> pcr.seqs(fasta= mme\_wd\_fasta.trim.contigs.fasta, count=** **mme\_wd\_fasta.contigs.count\_table,oligos=oligos16.txt, pdiffs=2, rdiffs=2)** This is where the issue begins. ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [September 30, 2025, 1:14pm UTC](https://forum.mothur.org/t/error-during-pcr-seqs-step-error-in-reading-your-fastafile-at-position-1-blank-name/22364/4 "2025-09-30T13:14:20Z")
Hmmm, that all seems right. Can you possibly post the content of your oligos16.txt file? Pat ---
**Author:** ![sbelz](https://avatars.discourse-cdn.com/v4/letter/s/94ad74/32.png) [@sbelz](https://forum.mothur.org/u/sbelz)\ **Post date:** [September 30, 2025, 1:33pm UTC](https://forum.mothur.org/t/error-during-pcr-seqs-step-error-in-reading-your-fastafile-at-position-1-blank-name/22364/5 "2025-09-30T13:33:46Z")
So my oligos16.txt file just has the primer sequences copy pasted as written above. ![Screenshot 2025-09-30 at 9.30.46 AM](https://canada1.discourse-cdn.com/flex036/uploads/mothur/original/1X/aa08ed557c15bcdc0563b4193e5c71d286768cf5.png) This command failed before and the issue I’m posting about is what occurred when I tried to rerun the command… I am wondering at this point if I ought to just restart the pipeline? I can’t remember the issue when it first failed (it was not this same one), but I remember the Mothur.exe file being closed when it shouldn’t have been and no listing of output files. ---
**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\ **Post date:** [October 1, 2025, 1:22pm UTC](https://forum.mothur.org/t/error-during-pcr-seqs-step-error-in-reading-your-fastafile-at-position-1-blank-name/22364/6 "2025-10-01T13:22:11Z")
The error you are getting seems to indicate an issue reading the fasta file, but the summary.seqs command is able to read it without failing. I would be happy to troubleshoot this for you. Could you send your fasta and count files to [mothur.westcott@gmail.com](mailto:mothur.westcott@gmail.com)? ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [October 11, 2025, 1:22pm UTC](https://forum.mothur.org/t/error-during-pcr-seqs-step-error-in-reading-your-fastafile-at-position-1-blank-name/22364/7 "2025-10-11T13:22:30Z")
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