Illumina basemount copy files error

Question

[anastazie.d]

Hello everyone!

I started to use basemount, which is command line tool to access data on BaseSpace.

I first mount filesystem and then use cp command to copy file to my computer.

Copy of some files is OK, but for approximately 1/3 files I get following error:

cp: error reading '/home/nasta/Public/BaseSpace/Projects/Haloplex/Samples/Hi5-1/Files/Data/Intensities/BaseCalls/Hi5-1_S2_L001_R2_001.fastq.gz': Bad address
cp: failed to extend '/home/nasta/Illumina_data/Hi5-1_S2_L001_R2_001.fastq.gz': Bad address

I checked file and it exists in that directory. I am able to unzip and open this file.

Did anyone had the same problem?

How did you overcome it?

Thanks,

Nastia

[Pierre Lindenbaum]

Please show us the output of

ls -la "/home/nasta/Public/BaseSpace/Projects/Haloplex/Samples/Hi5-1/Files/Data/Intensities/BaseCalls/Hi5-1_S2_L001_R2_001.fastq.gz"

[anastazie.d]

ls -la "/home/nasta/Public/BaseSpace/Projects/Haloplex/Samples/Hi5-1/Files/Data/Intensities/BaseCalls/Hi5-1_S2_L001_R2_001.fastq.gz"

-r--r--r-- 1 nasta nasta 98851092 Sep 26 07:45 /home/nasta/Public/BaseSpace/Projects/Haloplex/Samples/Hi5-1/Files/Data/Intensities/BaseCalls/Hi5-1_S2_L001_R2_001.fastq.gz

Answer 1

[anastazie.d]

Hi,

Finally I solved this problem with brute force approach.

I checked if the files were truncated by:

gunzip --test file.fastq.gz

Then I downloaded truncated files manually.