fastq-dump errors

jpmatteson · 03-30-2016, 08:51 PM

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.)

simonandrews · 04-01-2016, 06:51 AM

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 :-(

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03-30-2016, 08:51 PM	#1
jpmatteson Junior Member Location: Madison, WI Join Date: Sep 2015 Posts: 5	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.)

04-01-2016, 06:51 AM	#2
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	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 :-(