<p>As explained in the <a href="https://pepkit.github.io/docs/sample_annotation/" rel="nofollow noreferrer">pep docs</a>, the <code>sample_name</code> column should be considered a unique identifier for a sample. The PEP requires that <strong>One row corresponds to one sample</strong> You have multiple rows with the same name; this is not allowed.</p>

<p>You simply need to recast your annotation sheet such that it has <code>file1</code> and <code>file2</code> columns, but only 2 rows.</p>

CC BY-SA 3.0
2018-01-18T01:16:24.287Z
2018-01-18T08:00:34.270Z
2018-01-18T08:00:34.270Z
nsheff
<p>I am using <a href="https://github.com/pepkit/looper" rel="nofollow noreferrer">Looper</a>. While running <code>looper run project_config.yaml</code> I am getting <code>duplicate sample name</code> error. I have two <code>fastq</code> files for each sample, so in the <code>annotation.csv</code> file I have:</p>

<pre><code>sample_name,library,file
abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r1.fq.gz
abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r2.fq.gz
abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r1.fq.gz
abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r2.fq.gz
</code></pre>

<p>My <code>pipeline_interface.yaml</code> file looks the following way:</p>

<pre><code>protocol_mapping:
  RNA-seq: sandro_rna_seq

pipelines:
  sandro_rna_seq:
    name: sandro_rna_seq
    path: sandro_rna_seq.py  # relative to this 
pipeline_interface.yaml file
    looper_args: True
    arguments:
      "-L": "IU"
      "-T": "gencode_mouse_m13"
      "-E": "/scratch/nv4e/binf-
pipelines/bulk_rna_seq/salmon/pypiper/jyvo_experiment-metadata.yaml"
      "-C": "/scratch/nv4e/binf-
pipelines/bulk_rna_seq/salmon/pypiper/salmon_rna_seq.yaml"
      "-X": "True"
      "-P": "6"
      "-I": sample_name
    resources:
      default:
        file_size: "0"
        cores: "20"
        mem: "120000"
</code></pre>

<p>Why am I getting this error? How could I fix it?</p>

<scrnaseq><looper><yaml>
Looper: Duplicate sample name error
# Looper: Duplicate sample name error

(Asked by: username_0 on 2018-01-18)

I am using Looper. While running looper run project_config.yaml I am getting duplicate sample name error. I have two fastq files for each sample, so in the annotation.csv file I have:
sample_name,library,file
abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r1.fq.gz
abeta-24-1,RNA-seq,data/merged/abeta_24h_1_r2.fq.gz
abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r1.fq.gz
abeta-24-2,RNA-seq,data/merged/abeta_24h_2_r2.fq.gz

My pipeline_interface.yaml file looks the following way:
protocol_mapping:
  RNA-seq: sandro_rna_seq

pipelines:
  sandro_rna_seq:
    name: sandro_rna_seq
    path: sandro_rna_seq.py  # relative to this 
pipeline_interface.yaml file
    looper_args: True
    arguments:
      "-L": "IU"
      "-T": "gencode_mouse_m13"
      "-E": "/scratch/nv4e/binf-
pipelines/bulk_rna_seq/salmon/pypiper/jyvo_experiment-metadata.yaml"
      "-C": "/scratch/nv4e/binf-
pipelines/bulk_rna_seq/salmon/pypiper/salmon_rna_seq.yaml"
      "-X": "True"
      "-P": "6"
      "-I": sample_name
    resources:
      default:
        file_size: "0"
        cores: "20"
        mem: "120000"

Why am I getting this error? How could I fix it?

**Tags:** scrnaseq, looper, yaml

---

## 1 answers

### Answer by username_1 on 2018-01-18. Score: 2 | Accepted answer

As explained in the [pep docs](https://pepkit.github.io/docs/sample_annotation/), the `sample_name` column should be considered a unique identifier for a sample. The PEP requires that **One row corresponds to one sample** You have multiple rows with the same name; this is not allowed.

You simply need to recast your annotation sheet such that it has `file1` and `file2` columns, but only 2 rows.


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