Fasterq-dump unexpected parameter error (unexpected parameter[256]: '/home/GEOdata/sra/SRR6687807.sra)

Question

[cwliu0222]

Hi,

I ran "cat <myacclist.txt> | xargs -I{} prefetch {}" followed by "fasterq-dump /home/GEOdata/sra/*.sra" to download GEOdataset. However, It appeared " unexpected parameter[256]: '/home/GEOdata/sra/SRR6687807.sra'" while I ran the command "fasterq-dump /home/GEOdata/sra/*.sra."

I totally have no idea what it means. Does anybody with a similar experience, and please advise me to resolve it? Thank you.

[GenoMax]

Instead of fasterq-dump /home/GEOdata/sra/.sra you may have to try fasterq-dump /home/GEOdata/sra/*.sra. See if that works.

[GenoMax]

Looks like you tried this and it must not work. Do you actually have the SRA files downloaded? What is the output of ls -lh /home/GEOdata/sra/*.sra?

[cwliu0222]

I typed: ls -lh /home/GEOdata/sra/*.sra, it appeared /home/GEOdata/sra/SRR<different numbers="">.sra.

[GenoMax]

I assume this means that you had a number of files listed on individual lines (not what you literally put above). If so are you able to run just one file and try dumping the reads?

[cwliu0222]

Below is the link of the image which appeared that I typed ls -1h /home/GEOdata/sra/*.sra

https://ibb.co/922QHD9

[GenoMax]

Good so you have the files downloaded ok. So you should be able to do:

for i in *.sra; do fasterq-dump ${i} -O /a_directory_you_want; done

Check the available options for fasterq-dump and add any you need in the command above.

[arctic]

When running below with fastq-dump:

./sratoolkit.3.0.0-ubuntu64/bin/fastq-dump ./sra/*.sra --gzip --split-3 --outdir ./Q/

I also faced the "unexpected parameter[256]" for a SRR file. I have used a similar code successfully on a mac [sratoolkit.2.9.6-1-mac64] and a different set of SRR files before.

If I moved the SRR file mentioned after [256] to another folder:

1. Command above could convert that SRR file to fastq without a problem [So the file is fine].
2. Command on the parent folder would still throw the [256] error but for the immediate next SRR file after the one moved out.

I speculate the error is somehow about how fastq-dump delegates files (maybe for parallel computing?).

As GenoMax recommends above, a forloop (below) worked. Took overnight for 630+ SRR files:

for i in ./sra/*.sra

do

./sratoolkit.3.0.0-ubuntu64/bin/fastq-dump $i --gzip --split-3 --outdir ./Q/

done

[ATpoint]

Use GNU parallel to do that in some parallel fashion rather than 1:1 with a loop if you want to speed that up and have the CPU and disk resources for it. Or just directly download fastq files via sra-explorer.info

[cwliu0222]

Thank you for replying. Sorry, I made a typo. I tried: fasterq-dump /home/GEOdata/sra/*.sra But it appeared the unexpected parameter[256] as I described above.