Error with VelvetOptimiser

[ClemBuntu]

Hello all,
I'm using VelvetOptimiser.pl from k-mer size 19 to 35 and I got the following errors ;

Velveth failed! Response:
1
mars 2 13:16:55 Velveth with hash value 21 finished.
Velveth failed! Response:
1
mars 2 15:04:23 Velveth with hash value 27 finished.
Velveth failed! Response:
1
mars 2 15:22:32 Velveth with hash value 31 finished.

I had a look to the source code and that didn't help me :

unless(-r ($prefix . "_data_$hv" . "/Roadmaps")){
print STDERR "Velveth failed! Response:\n$vhresponse\n";

What does " unless -r" mean ? Oo

Anyway, here's the log file if it can help ;

User specified velvetg options: -exp_cov 400 -ins_length 400
mars 2 12:08:30
Will run velvet optimiser with the following paramters:
Velveth parameter string:
-separate -fastq -shortPaired allReads_R1.fastq allReads_R2.fastq
Velveth start hash values: 19
Velveth end hash value: 35
Velveth hash step value: 2
Velvetg minimum coverage cutoff to use: 0

User specified velvetg options: -exp_cov 400 -ins_length 400
Read tracking for final assembly off.
mars 2 12:08:30

Beginning velveth runs.
********************************************************
Assembly id: 2
Velveth timestamp: mars 2 2015 13:16:42
Velveth version: 1.2.10
Readfile(s): -separate -fastq -shortPaired allReads_R1.fastq allReads_R2.fastq
Velveth parameter string: auto_data_21 21 -separate -fastq -shortPaired allReads_R1.fastq allReads_R2.fastq
Assembly directory: /data/Velvet/Sample_allReads/auto_data_21
Velvet hash value: 21
**********************************************************
********************************************************
Assembly id: 5
Velveth timestamp: mars 2 2015 15:04:14
Velveth version: 1.2.10
Readfile(s): -separate -fastq -shortPaired allReads_R1.fastq allReads_R2.fastq
Velveth parameter string: auto_data_27 27 -separate -fastq -shortPaired allReads_R1.fastq allReads_R2.fastq
Assembly directory: /data/Velvet/Sample_allReads/auto_data_27
Velvet hash value: 27
**********************************************************
********************************************************
Assembly id: 7
Velveth timestamp: mars 2 2015 15:22:29
Velveth version: 1.2.10
Readfile(s): -separate -fastq -shortPaired allReads_R1.fastq allReads_R2.fastq
Velveth parameter string: auto_data_31 31 -separate -fastq -shortPaired allReads_R1.fastq allReads_R2.fastq
Assembly directory: /data/Velvet/Sample_allReads/auto_data_31
Velvet hash value: 31

Please note VelvetOptimiser is still running that's why not all hash failed (not yet ?).

[mastal]

Are you getting any files produced in any of your velvet output directories?

If velveth runs successfully you should get 3 files, called Sequences, Roadmaps, and Log.

Have you tried running velvet without velvet optimiser to check that it is properly installed?

[ClemBuntu]

I only have Sequences and Log but not Roadmaps.

I'm gonna use velvet withouh velvet optimiser and I give you informer.

[ClemBuntu]

Hello,
So velvet without velvet optimiser does work.
Strangly after lauching velvetOptimiser and typping "ps -u" command I get this ;

PID TTY TIME CMD
12260 ? 00:00:00 time
12261 ? 00:00:01 VelvetOptimiser
12314 ? 00:44:39 velveth <defunct>

which means velveth was a zombie .... That's very strange oO
Any ideas anyone ?

Edit ;
velvetOptimiser has created several repositories like auto_data_kmersize and I don't know why but some of them contains a Roadmaps file, some on them no...