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Problem using SRAtoolkit

Hello Biostars community

I wanted to use split-3 function of sratoolkit to split my pair-ended RNA-seq files to two fastq files. However, after inserting the code, I get the following error. What is the problem?

./fastq-dump --split-3
2023-01-29T12:54:14 fastq-dump.3.0.2 err: param empty while validating argument list - expected accession
sra sratoolkit fastq rna-seq
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updated by Ram Ram • written by Yoosef • Yoosef

1 answer

Message tells you what you need to do. You need to provide an SRA accession number or name of a downloaded .sra file with this command.

e.g. fastq-dump --split-3 SRR345355

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written by GenoMax GenoMax

Thanks for your help. Actually I was trying to use following loop to split my SRA files. However, I think the problem relates to my file extensions as they don't have .sra. How can I add that to the end of all my files?

for i in /media/yousef/C0B0499AB04997B4/transcriptom_files/* ; do ./fastq-dump --split-3 --outdir /media/yousef/C0B0499AB04997B4/split/$i; done
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written by Yoosef • Yoosef

Did you download the files from SRA using prefetch?

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written by GenoMax GenoMax

No. I downloaded them by clicking on download link in NCBI website.

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written by Yoosef • Yoosef

Try processing one file and see it works before you try the loop. In case your files are corrupt this is not going to work.

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written by GenoMax GenoMax

Sure. Thanks for your help.

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written by Yoosef • Yoosef

If you are sure the files are in .sra format then you could rename one file and try. Something like

mv file file.sra
fastq-dump --split-3 file.sra

I suggest you try instead

fastq-dump --split-files file.sra
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written by GenoMax GenoMax

Thanks. Yes files are in sra format. I could solve this by adding a .sra to each file. I was just wondering, is there a way to add .sra to all files by using a code in linux?

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written by Yoosef • Yoosef 
for i in /media/yousef/C0B0499AB04997B4/transcriptom_files/* ; do echo mv ${i} $[i}.sra; done

If all commands look correct then remove echo to actually do the renaming.

If you want to be super careful the you could cp ${i} ${i}.sra (instead of mv command) leaving a copy of original files intact.

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written by GenoMax GenoMax

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