FTP transfer - corrupt files at other end

[bio_informatics]

Hello members,

I've 218 genome (E. coli) files - 436 fastq.gz files.

I created their symbolik links in one folder (as they are scattered over multiple sequencing folders and different depths of directory), and sent them using bash script via FTP utility.

I do not get any error, warning or whatsoever during transfer. I can see their size at FTP web interface as in on command line interface on my end.

But the data on the other end is corrupted.
I'm unable to understand what might be causing this, and how should I fix this?

Please guide.

[Richard Finney]

Did you set "binary on" ?

You have to set "binary on" when using FTP.

[bio_informatics]

Did you set "binary on" ?

You have to set "binary on" when using FTP.

Hi Richard,
Thanks for your reply.
It by default says:

Uploading in BINARY file XTGEN_20121130_SN180_IL100028322_TTGGTATG-FMC_UTI_01875_L004_R1_trimmed.fastq.gz

[GenoMax]

What FTP program are you using? Some FTP programs can't follow soft-links correctly.

[bio_informatics]

What FTP program are you using? Some FTP programs can't follow soft-links correctly.

Hello genomax,
FTP linux utility.

[GenoMax]

Have you tried sftp instead of plain ftp?

[bio_informatics]

Have you tried sftp instead of plain ftp?

Hi,

I cannot use CURL, stfp as the user name I've has already an @ in it, and thus, many command line transfer utilities refuse to accept it.

something like:

user@group_name

[GenoMax]

Can you clarify what you are trying to do?

Is this transfer between servers i.e. you have created a symlinked folder of files on server A that you are trying to get at from server B (via the web?).

[bio_informatics]

Can you clarify what you are trying to do?

Is this transfer between servers i.e. you have created a symlinked folder of files on server A that you are trying to get at from server B (via the web?).

Hi Genomax,
I created symlinks at remote server A.
Wrote bash script at Server A, with FTP which uses - password, username of Server B. This bash script loops over .fastq.gz files (which are symlinks here).

Folder:
-->has 436 symlinks..

From Server A fastq.gz -->FTP Server B

bash script.sh inside the symlinks folder.

[GenoMax]

Hi,

I cannot use CURL, stfp as the user name I've has already an @ in it, and thus, many command line transfer utilities refuse to accept it.

something like:

user@group_name

Try the options included here to handle the @ for sftp: http://unix.stackexchange.com/questi...ontains-symbol