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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.

Describe your issue in detail

• Please copy and paste the command you ran and the error information if reported.
• It would be more helpful to provide as much information as you can:
  • Are you running on a personal computer or a server?
  • What's the operating system, and how much RAM (memory) is available?
  • Show the types and sizes of input files with file xxx and ls -lh xxx.
  • Show some lines of input files with head -n 5 xxx or zcat xxx.gz | head -n 5.
• Provide a reproducible example.
  • Has this problem happened many times?
  • Or it only failed with this input file or/and these command/parameters.

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