Any ideas on what can be causing the following file corruption?
Path 1
- I have a
example.fastq.gz
file on remote server. - I upload it to usegalaxy.eu using
curl -T {"example.fastq.gz"} --user user@name.de --ssl ftp://ftp.usegalaxy.eu
- I import it to galaxy setting it’s datatype to
fastq.gz
- I execute fastQC on it and end up with
Ran out of data in the middle of a fastq entry. Your file is probably truncated
orID line didn't start with '@'
- I download the
example.fastq.gz
from Galaxy to disk - I run
gunzip
on the file and getunexpected end of file
uncompress failed
Path 2
- I have a
example.fastq.gz
file on remote server (this is identical file from Path 1) - I use scp to copy it to my local disk
- I use
gunzip
to extract it - I run fastQC locally
- All works fine
edit: the md5 has changed
original
md5sum CB1A1_S1_R2_001.fastq.gz
33462a19ef9cb2595ffa06a849b062ff CB1A1_S1_R2_001.fastq.gz
downloaded from usegalaxy.eu
md5 CB1A1_S1_R2_001.fastq.gz
MD5 (CB1A1_S1_R2_001.fastq.gz) = 45284f73109d8866cfe81f3cdb2014ca