Hello Everyone,
I'm trying to convert SRR121576, SRR121577, SRR121578, SRR121579 files to fastq format. I am using ubuntu software and after a long way searching web I found some commands and I tried fastq-dump -A SRR121576 -D SRR121576.sra Command And I got
2014-08-13T08:53:37 fastq-dump.2.1.7 err: option -D is deprecated, see --help
2014-08-13T08:53:38 fastq-dump.2.1.7 err: data bad version while constructing page map within virtual database module - failed SRR121576.sra
I also tried fastq-dump --split-files -A SRR121576.sra and I got
014-08-13T08:54:49 fastq-dump.2.1.7 err: data bad version while constructing page map within virtual database module - failed SRR121576.sra
Written 0 spots total
But after I failed, I tried only searching web to find directly .fastq after seaching I found ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/SRR121577/ this ftp but when I tried to gunzip or archivemanager or winrar with wine all of them failed because of this files corrupted. I tried download again but also it did not work. To sum up, I need these files as .fq formatted to do tuxedo software (I do not now any different way to rna-seq analyzing) Can you help me anyway to repair archive or to find new fastq file or convert sra to fastq.
Thank you :)
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Veli Kaan Aydin •
Go to EBI http://www.ebi.ac.uk/ena/data/view/SRR121576
They have fastq files ready for you.
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Ming Tommy Tang
This way is better than fastq-dump. EBI has fastq files to squarely download and use.
I suggest downloading the latest sratoolkit from http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software (which is currently, 2.3.5-2).
Now, either:
path/to/sratoolkit.2.3.5-2-centos_linux64/bin/fastq-dump SRR121576.srapath/to/sratoolkit.2.3.5-2-centos_linux64/bin/fastq-dump SRR121576, which downloads and convert.Useful options:
--gzip will gzip the fastq--split-3 is for paired end readsHello Sebastian,
First thank you for answer, I already download and install latest version (Also I configured it as they so ) But still I get errors while I'm trying codes I still gets those errors.
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Veli Kaan Aydin •
Mmh weird. It worked for me. You downloaded your file from EBI, right? Maybe the sra file stored there is somehow corrupted as Devon wrote above. I downloaded via the link provided at the NCBI SRA page for the sampel which is:
wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR121/SRR121576/SRR121576.sra
You might want to try that.
Yes, I tried that source but I'm going to try all of it again.
Thanks :)
How do I know that fastq-dump is using my downloaded sra object (following the 1st path but not the 2nd one)
FYI, I've moved this to an answer, hope you don't mind.
Download sra-toolkit from NCBI SRA. Download the runs you want from NCBI SRA if you don't have them already.
Use the syntax: fastq-dump <yourFileHere.sra>. Add --split-files if you're dealing with paired-end reads.
I'm looking at the documentation and the -A & -D aren't listed as valid options... http://www.ncbi.nlm.nih.gov/Traces/sra/?view=toolkit_doc&f=fastq-dump
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Jeff Stafford •
Thank you for answering my question, and I know it is not listed but since I'm trying the commands I already try lots of them :/
Totally understand the feeling... once I spent two or three days trying to get the fastx-toolkit to work only to find that it needs the secret "-Q33" option before it can read new Illumina files. Of course this option/issue wasn't in any of the documentation and I spent days bashing my head into the keyboard until I stumbled on a well-hidden forum post that mentioned it.
I always use the command and it has always worked
fastq-dump --split-3 *.sra
For any kind of .sra file, if its single end then one output as .fastq and if its paired end then `_1.fastqand*_2.fastq` is reported in your same directory.
HTH
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Manvendra Singh
Hi sorry to bother you...I use the command fastq-dump --split-3 *.sra
The problem is for the single end it works but for the paired end it doesn't work ...
It throws the error: data bad version while constructing page map within virtual database module - failed
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caelyn5201314 •
See if there's a newer version of fastq-dump. They update it on occasion and there's little in the way of backwards compatibility (one of the many reasons people try to avoid SRA format).
thank you very much !!! It worked !!!
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I'm trying to download the archive and unpacking it. I'll let you know
FYI, I've gotten a few "corrupted files" from ENA that turned out to have been submitted that way.
Thank you for information, I'm trying wynstep's and Boegel's answer I hope I'll find solution.