SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SRA to fastq conversion with fastq-dump loses sequences pcantalupo Bioinformatics 13 10-08-2015 04:09 PM
fastq-dump transforu Bioinformatics 5 12-11-2014 09:22 AM
Convert SRA to FASTQ with fastq-dump but problem of read length MurielGB Illumina/Solexa 9 10-07-2014 09:10 AM
fastq-dump for Illumina duygu Bioinformatics 3 08-03-2011 02:00 PM
Fastq-dump.exe Giles Bioinformatics 2 06-11-2011 12:34 PM

Reply
 
Thread Tools
Old 03-30-2016, 07:51 PM   #1
jpmatteson
Junior Member
 
Location: Madison, WI

Join Date: Sep 2015
Posts: 5
Default fastq-dump errors

I'm getting two errors on certain fastq-dump jobs. I am submitting jobs to HTCondor using a dag file to manage downloads. I am queuing multiple jobs and sometimes I get the following errors:

2016-03-31T03:17:24 fastq-dump.2.5.7 err: file unauthorized while opening file within network system module - log failure: RC(
rcText,rcString,rcConverting,rcBuffer,rcInsufficient) in 'error with http open '$(U)''
2016-03-31T03:17:24 fastq-dump.2.5.7 err: item not found while constructing within virtual database module - the path 'SRR0593
27' cannot be opened as database or table

The strange thing is that sometimes I get the errors and sometimes I don't, even for the same files. For instance if I download 10 files, and 5 return these errors, if I submit the same ten jobs again, some or all of the files which gave errors might download normally. I'm very confused about this, any suggestions would be great. (I think the second error is the result of the first because these files seem to exist.)
jpmatteson is offline   Reply With Quote
Old 04-01-2016, 05:51 AM   #2
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
Default

If it's any consolation we gave up trying to understand all of the fastq-dump errors we saw and we now have a loop in our pipeline which simply tries the command again (up to 5 times) before deciding that there really is an error. a scary number of fastq-dump errors are not reproducible :-(
simonandrews is offline   Reply With Quote
Reply

Tags
bioinformatics, sratoolkit fastq-dump

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:10 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO