Question: Errors with SRA-toolkit: not enough space on the disk. (112)
1
gravatar for olive1212
18 days ago by
olive121240
olive121240 wrote:

SOLVED (09.08.19): I was trying to save to hard drives with Fat32 file system, which has wont save files >4Gb. Reformatted the hard drive, and the files downloaded. Thank you for everyone' help!

I keep having issues when downloading datasets with SRA. This dataset I tried to download below is about 16Gb and it seems to fail after 3-4Gb downloads. Error says There is not enough space on the disk.(112), but I have it downloading on a 1Tb hard drive. Any suggestions?

C:\Users\USER\Downloads\sratoolkit.2.9.6-1-win64\bin>prefetch.exe -O "F:\ProjectSRAFiles" -X 100G -v SRR#

2019-09-05T19:10:10 prefetch.2.9.3: KClientHttpOpen - connected from 'IP ADDRESS' to www.ncbi.nlm.nih.gov (IP ADDRESS)
2019-09-05T19:10:11 prefetch.2.9.3: KClientHttpOpen - verifying CA cert
2019-09-05T19:10:11 prefetch.2.9.3: KClientHttpOpen - connected from 'IP ADDRESS' to sra-download.ncbi.nlm.nih.gov (IP ADDRESS)
2019-09-05T19:10:11 prefetch.2.9.3: KClientHttpOpen - verifying CA cert
2019-09-05T19:10:11 prefetch.2.9.3: 1) Downloading 'SRR#'...
2019-09-05T19:10:14 prefetch.2.9.3:  Downloading via https...
2019-09-05T19:10:14 prefetch.2.9.3: https://sra-download.ncbi.nlm.nih.gov/traces/sra61/SRR/006699/SRR# -> /f/ProjectSRAFiles/SRR#.sra.tmp.7523.tmp
2019-09-05T19:10:14 prefetch.2.9.3: KClientHttpOpen - connected from 'IP ADDRESS' to sra-download.ncbi.nlm.nih.gov (IP ADDRESS)
2019-09-05T19:10:14 prefetch.2.9.3: KClientHttpOpen - verifying CA cert
2019-09-05T19:13:16 prefetch.2.9.3 err: unknown while writing file within file system module - error writing system file - There is not enough space on the disk.(112)
2019-09-05T19:13:16 prefetch.2.9.3 int: unknown while writing file within file system module - Cannot KFileWrite: /f/ProjectSRAFiles/SRR#.sra.tmp.7523.tmp
2019-09-05T19:13:18 prefetch.2.9.3: 1) failed to download SRR#

UPDATE (09.06.19): Now with aspera fasp download, I am not even getting an error. Just a message that the download fails after downloading only ~4.5Gb of the data. I have tried a brand new hard drive, and it is the same problem so I don't think it is an issue of file size.

USER-MacBook-Pro-2:ncbi USER$ prefetch -v SRR#

2019-09-06T15:34:36 prefetch.2.9.3: Using '/Users/USER/Applications/Aspera Connect.app/Contents/Resources/ascp'
2019-09-06T15:34:36 prefetch.2.9.3: KClientHttpOpen - connected from 'IP ADDRESS' to www.ncbi.nlm.nih.gov (IP ADDRESS) 
2019-09-06T15:34:36 prefetch.2.9.3: KClientHttpOpen - verifying CA cert 
2019-09-06T15:34:36 prefetch.2.9.3: KClientHttpOpen - connected from 'IP ADDRESS' to sra-download.ncbi.nlm.nih.gov (IP ADDRESS) 
2019-09-06T15:34:36 prefetch.2.9.3: KClientHttpOpen - verifying CA cert 
2019-09-06T15:34:37 prefetch.2.9.3: KClientHttpOpen - connected from 'IP ADDRESS' to www.ncbi.nlm.nih.gov (IP ADDRESS) 
2019-09-06T15:34:37 prefetch.2.9.3: KClientHttpOpen - verifying CA cert 
2019-09-06T15:34:37 prefetch.2.9.3: 1) Downloading 'SRR#'...
2019-09-06T15:34:37 prefetch.2.9.3:  Downloading via fasp...
/Users/USER/Applications/Aspera Connect.app/Contents/Resources/ascp /Users/USER/Applications/Aspera Connect.app/Contents/Resources/ascp -i /Users/USER/Applications/Aspera Connect.app/Contents/Resources/asperaweb_id_dsa.openssh -pQTk1 -l 450m dbtest@sra-download.ncbi.nlm.nih.gov:data/sracloud/traces/sra61/SRR/006699/SRR# /Volumes/USER/CTAProjectSRAFiles/ncbi/public/sra/SRR#.sra.tmp.16642.tmp
SRR#                                      
2019-09-06T15:46:15 prefetch.2.9.3:  fasp download failed
2019-09-06T15:46:15 prefetch.2.9.3: 1) failed to download SRR#
software error • 254 views
ADD COMMENTlink modified 14 days ago • written 18 days ago by olive121240
2

Open sratoolkit options vdb-config.exe -i to check if the default download path is set to the 1Tb hard drive.

ADD REPLYlink written 18 days ago by arup1.7k

It is set to the correct hard drive

ADD REPLYlink modified 17 days ago • written 18 days ago by olive121240
2

Do yourself a favor and get a small Linux VM or partition and then simply download directly as fastq: Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD REPLYlink written 17 days ago by ATpoint23k

The sequences I am trying to download are not on ENA (yet?)

ADD REPLYlink written 17 days ago by olive121240

That is unfortunate. Still, the error message is clear, your disk is full. In the linked tutorial there is also a suggestion on how to efficiently use prefetch/parallel-fastq-dump, the paragraph starts with Edit 28.2.19: For matters of completeness. I suggest you do the download chunkwise, so get a sra file, convert to fastq, remove sra, maybe save fastq somewhere else to free disk space. As said, the tutorial is for Unix so you would probably need a VM.

ADD REPLYlink written 17 days ago by ATpoint23k
1

It is not only a matter of setting a correct download directory. A temporary directory also must have enough disk space. See this thread for more information.

It says clearly in the message above that /f/ProjectSRAFiles/SRR#.sra.tmp.7523.tmp can't be written, meaning that /f/ProjectSRAFiles/ likely does not have enough space. I would make sure that old or incomplete downloads are purged from that directory as well.

ADD REPLYlink written 17 days ago by Mensur Dlakic1.3k

The hard drive reports having plenty of space, and all incomplete files have been removed (I checked for hidden files as well).

ADD REPLYlink written 17 days ago by olive121240

Be also sure to deactivate the caching option in vdb-config. I cannot even tell you what exactly these cache files are that prefetch saves on disk, but they are large and take up space while not necessary for proper download.

ADD REPLYlink written 17 days ago by ATpoint23k

Can you share the accession number? Alternatively, contact the NCBI support.

ADD REPLYlink written 15 days ago by ATpoint23k

Please add:

I was trying to save to hard drives with Fat32 file system, which has wont save files >4Gb. Reformatted the hard drive, and the files downloaded.

as an answer so closure can be provided to this thread.

ADD REPLYlink written 15 days ago by genomax71k
4
gravatar for olive1212
14 days ago by
olive121240
olive121240 wrote:

I was trying to save to hard drives with Fat32 file system, which has wont save files >4Gb. Reformatted the hard drive, and the files downloaded. Thank you for everyone' help!

ADD COMMENTlink written 14 days ago by olive121240
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