How to convert fasterq File into fastq files ?
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10 weeks ago
NikhilP ▴ 20

So I have two fasterq files such as :-

20900104398_S66_L001_R1_001.fasterq
20900104398_S66_L001_R2_001.fasterq

I want to convert them into fastq files so that I can start doing downstream analysis in my pipeline. I tried using fasterq-dump (as it was the only thing I found until now). But using that is giving me an error

2022-11-15T07:14:08 fasterq-dump.3.0.0 err: name not found while resolving query within virtual file system module - failed to resolve accession '/mnt/hdd/Data/20900104398_S66_L001_R1_001' - Cannot resolve accession ( 404 )
2022-11-15T07:14:08 fasterq-dump.3.0.0 err: extract_acc2( '/mnt/hdd/Data/20900104398_S66_L001_R1_001' ).VFSManagerExtractAccessionOrOID() -> RC(rcVFS,rcPath,rcConstructing,rcParam,rcIncorrect)
fasterq-dump quit with error code 3

Is there any other tool to convert them?

Thank you!

fastq fasterq • 442 views
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Just to clarify, are you downloading data from NCBI, because it seems to me that this is data (based on file name) right from a local sequencer?

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No, I didn't download the data from NCBI. The client gave it to me.

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Then you don't have to run this tool. fasterq-dump is a tool to fetch published NGS data from NCBI. What did you expect would it do?

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Does head 20900104398_S66_L001_R1_001.fasterq show binary characters like example here Tools for fasterq file? ?

What does the command file 20900104398_S66_L001_R1_001.fasterq show?

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Yes the command head 20900104398_S66_L001_R1_001.fasterq is showing just like the link to attached.

And file 20900104398_S66_L001_R1_001.fasterq is showing 20900104398_S66_L001_R1_001.fasterq: Progressive Graphics image data,

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We have two examples of files (one from other thread) in a previously unseen format. What kind of sequencer is this data from (file name seems to be in Illumina format)? I wonder if it is from a new batch of sequencers that were recently announced. If so it may need re-processing to generate sequence data.

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the error looks like more a filesystem problem than a software error

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Okay. This is the first time I have encountered this type of filetype. So the error is also confusing.

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