Lumpy preprocessing: empty output

usegalaxy.eu support
1

Dear usegalaxy team,

The Lumpy preprocessing tool runs successfully, but generate three empty datasets. I think these lines from the standard error might explain the issue. Could you please, check?
Thank you!

History API ID aab52abe370e60be
Job API ID: 11ac94870d0bb33a9add9e5560333e8c

samblaster: Version 0.1.26
samblaster: Inputting from stdin
samblaster: Outputting to stdout
[E::bgzf_flush] File write failed (wrong size)
samtools collate: Couldn't write to intermediate file "/tmp/collate23496a.0010.bam": 
No space left on device
2

Hi @BorisRJ,
the Galaxy server had an issue that caused that problem. Could you try again?

Regards

3

Dear @gallardoalba,

I am experiencing the same error that @BorisRJ described before.

History API ID: 21b5ffe354a03da3
History Content API ID: 11ac94870d0bb33a5be8df6955c0985b

samblaster: Version 0.1.26
samblaster: Inputting from stdin
samblaster: Outputting to stdout
[E::bgzf_flush] File write failed (wrong size)
samtools collate: Couldn’t write to intermediate file “/tmp/collate1f71b9.0032.bam”: No space left on device

Can you recommend a workaround?

4

Hello @BorisRJ How are you?
Did you solve this problem?
im having the same one.

Also: Is there any parameter to set in BWA-MEM in order to run LUMPY preprocessing or just default ones are ok?

my LUMPY preprocessing tool is not working and shows the same problem you mentioned

5

hello. The same error occuring with Lumpy preprocessing now.
how to proceed?

thanks in advance

6

Hi @felipeluz,
I’ll increase the Lumpy assigned memory; please try again tomorrow. Sorry for the late response @dmz.

Regards

7

Thak you so much.
i appreciate it.

ok, i’ll try again tomorrow.

Best regards,

1 Like
8

Hello CristĂłbal. How are you?
I’ve just tryed LUMPY preprocessing again on galaxy. The same error occured.

Just to know… LUMPY Preprocessing app is not working due to memory issues. If you could expand its memory too, i appreciate it.

Best regards,

9

Please…
The app with issues is LUMPY PREPROCESSING.
Can you increase it memory?

I’ve tried over and over again and it doesnt work.

regards,
Felipe

1 Like
10

Hi @felipeluz,
yes, I’m going to check that problem.

Regards