rmdup: dup-num-file not created if no duplicated reads

[fgvieira]

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Prerequisites

• Make sure you've installed the correct executable binary file.
  For Mac users, Please download
  • seqkit_darwin_amd64.tar.gz for Mac with Intel CPUs.
  • seqkit_darwin_arm64.tar.gz for Mac with M series CPUs.
• Make sure you are using the latest version by seqkit version -u.
• Read the usage and examples for the specific subcommand.

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  • Show the types and sizes of input files with file xxx and ls -lh xxx.
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I am running seqkit on a RedHat server:

seqkit rmdup --threads 10  --dup-num-file dup.tsv --ignore-case --by-seq  --out-file collapsed.fastq.gz collapsed.rmdup.fastq.gz

But seqkit rmdup does not create the dup-num-file (dup.tsv) file if there are no duplicated reads in the input file.

Input file is a FASTQ:

$ zcat collapsed.fastq.gz | head -n 8
@T0_RID60_S1_CM000682.2_ngsngs:13496936-13497014_length:79_mod0000 F2 R1 merged_79_0
TAAGGAAGCAGTGGAAAAAGAATAAATGCTGTAGATGAGGACAAGAAATTAGTTGAACTTTAATAAACTTCAAATGACT
+
CCCGGGGGG=GGGJJJGJGJJGJJJJJJGJCJJC=GJJJJJJGG1JGGGJJCGJJJG=JGGCGJCCJJGJJJGJGCCJG
@T2_RID60_S1_CM000666.2_ngsngs:130549431-130549518_length:88_mod0000 F3 R1 merged_88_0
TTTGCTCATATTTTGTGAAGTATTTTTATATCTGTATTCATGAATGATATTGCCATGCAATTGTCTTTTATTTTAATAATCTTGTCTT
+
CC8G=GGGGGGGGJJGJJJJJJJJJGCGGJJGJCJJJJJGJG8J1J=GJCJGJJJJJ(GGJGJGGJGGGGJJJJGJGGGCJJCJGGCJ

[shenwei356]

seqkit rmdup does not create the dup-num-file (dup.tsv) file if there are no duplicated reads in the input file.

Oh, yes, it's designed to act like this. https://github.com/shenwei356/seqkit/blob/master/seqkit/cmd/rmdup.go#L181

[fgvieira]

I can see the logic of not creating the file if there are no duplicated reads but, when using seqkit on a snakemake workflow, sometimes it crashes because the file is not created.
An alternative would be to create an empty file if there are no duplicates.

[shenwei356]

Well, I can change the behaviour. But it should be easy to detect if a file exists in snakemake with something like os.path.exists. If the file does not exist, just skip the downstream steps.

[shenwei356]

Changed. Try this.

• seqkit_darwin_arm64.tar.gz
• seqkit_linux_amd64.tar.gz
• seqkit_darwin_amd64.tar.gz

[fgvieira]

Nice! It seems to work!
thanks,