Question: Windows batch cmd for fastq-dump
0
gravatar for rrbutleriii
8 months ago by
rrbutleriii70
US, Chicago
rrbutleriii70 wrote:

For reasons outside my control, I have to fetch fastq files from sra on a Windows computer. Currently I have a list of SRRs in a file, and a batch cmd file:

for /F "tokens=*" %%X in (SRR_Acc_List.txt) do (
  prefetch %%X && vdb-validate %%X && fastq-dump [options] %%X
)

Which works I think, but I don't know if it will prevent the fastq-dump command if the vdb-validate function says the sra is corrupt. Does anyone know the exit status of vdb-validate when it completes but the validation failed?

fastq-dump windows sra • 374 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 8 months ago by rrbutleriii70

If you have to fetch fastq files then it would be much better to do so by getting them from EBI-ENA.

ADD REPLYlink modified 7 months ago • written 8 months ago by genomax69k

Wouldn't you believe the silliness of the situation, this machine also only has Internet Explorer, and won't allow java (or aspera connect). I would batch query the fastq files via ftp, but I want to verify file integrity after download using vdb-validate, as I had heard of incomplete transfers of fastq files resulting in corrupted data. Is there a way to obtain checksums on the fastqs?

ADD REPLYlink written 7 months ago by rrbutleriii70

Have you considered downloading on a different machine and then moving the data to this one, if you must use it?

ADD REPLYlink written 7 months ago by genomax69k

Indeed I have. This gets deep into the weeds of our institutional politics (of the type that would make Kafka blush). The short of it is this the actual server is airgapped, and virtual machine with internet access for the purposes of shuttling data is this one (a Win Server 2008 R2 OS, with heavily restricted privileges). I could daisy chain across three computers, but this does the trick, I just don't see the status of the vdb-validate if query a large batch.

Oh, and properly filled out request for service paperwork submitted to the appropriate group will sit in an inbox for three months before returning the response 'What is the NCBI?'. Meditation is important here :)

ADD REPLYlink written 7 months ago by rrbutleriii70
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