VelvetOptimiser

[Votinhkiem90]

tnt@Lam-Nguyen:~/Downloads/software/VelvetOptimiser-2.2.5$ VelvetOptimiser.pl -s 27 -e 31 -f '-shortPaired -fastq shuff_k8_q30.fastq' -t 4 --optFuncKmer n50

****************************************************
VelvetOptimiser.pl Version 2.2.4
****************************************************
Number of CPUs available: 4
Current free RAM: 2.425GB
Velvet OMP compiler setting: 1
Th10 4 12:08:52 Starting to check input parameters.
Velveth parameter string OK.
Th10 4 12:08:52 Finished checking input parameters.
Logfile name: 04-10-2013-12-08-52_Logfile.txt
Velvet details:
Velvet version: 1.2.09
Compiled categories: 2
Compiled max kmer length: 31
Maximum number of velvetinstances to run: 4
Will run velvet optimiser with the following paramters:
Velveth parameter string:
-shortPaired -fastq shuff_k8_q30.fastq
Velveth start hash values: 27
Velveth end hash value: 31
Velveth hash step value: 2
Velvetg minimum coverage cutoff to use: 0

Read tracking for final assembly off.
i is 27
i is 29
i is 31
Th10 4 12:08:52 Beginning velveth runs.
Th10 4 12:08:52 Running velveth with hash value: 27.
Th10 4 12:08:54 Running velveth with hash value: 29.
Th10 4 12:08:56 Running velveth with hash value: 31.
Th10 4 12:09:11 Velveth with hash value 27 finished.
Th10 4 12:09:12 Velveth with hash value 29 finished.
Th10 4 12:09:19 Velveth with hash value 31 finished.
Can't exec "velvetg": No such file or directory at VelvetOpt/gwrap.pm line 136.
Th10 4 12:09:19 Finished velveth runs.
Th10 4 12:09:19 Beginning vanilla velvetg runs.
Th10 4 12:09:19 Running vanilla velvetg on hash value: 27
Can't exec "velvetg": No such file or directory at VelvetOpt/gwrap.pm line 136.
Th10 4 12:09:19 Velvetg on hash value: 27 finished.
Th10 4 12:09:21 Running vanilla velvetg on hash value: 29
Can't exec "velvetg": No such file or directory at VelvetOpt/gwrap.pm line 136.
Th10 4 12:09:21 Velvetg on hash value: 29 finished.
Th10 4 12:09:23 Running vanilla velvetg on hash value: 31
Can't exec "velvetg": No such file or directory at VelvetOpt/gwrap.pm line 136.
Th10 4 12:09:23 Velvetg on hash value: 31 finished.
Use of uninitialized value in numeric ne (!=) at /usr/local/bin/VelvetOptimiser.pl line 282.
Use of uninitialized value in numeric gt (>) at /usr/local/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value in numeric ne (!=) at /usr/local/bin/VelvetOptimiser.pl line 282.
Use of uninitialized value $maxScore in numeric gt (>) at /usr/local/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value in numeric gt (>) at /usr/local/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value in numeric ne (!=) at /usr/local/bin/VelvetOptimiser.pl line 282.
Use of uninitialized value $maxScore in numeric gt (>) at /usr/local/bin/VelvetOptimiser.pl line 283.
Use of uninitialized value in numeric gt (>) at /usr/local/bin/VelvetOptimiser.pl line 283.
Th10 4 12:09:25 Hash value of best assembly by assembly score: 27
Th10 4 12:09:25 Optimisation routine chosen for best assembly: shortPaired
Th10 4 12:09:25 Looking for the expected coverage
Unable to open /home/tnt/Downloads/software/VelvetOptimiser-2.2.5/auto_data_27/stats.txt for exp_cov determination.
How to fix this bold error?

[sisch]

How to fix this bold error?

I'd say, by first fixing the real errors in your output. If you scan through your error log you will find that the execution of "velvetg" fails in all three cases. Thus, the problem is that VelvetOptimiser is not able to locate/execute the velvetg executable. As a consequence, there is of course no stats.txt as it is usually generated by velvetg.

Possible solutions:
1. Check the permissions of velvetg, maybe your Script is not allowed to run it.

ls -al `which velvetg`

2. Find out, whether your velvetg executable is in the PATH (if not the above might not have worked either.)by running

velvetg

If it doesn't run, you might want to reinstall velvet, correctly.

Disclaimer: I have never used the VelvetOptimiser script and just try to help you find the source of the problem

[Votinhkiem90]

I'd say, by first fixing the real errors in your output. If you scan through your error log you will find that the execution of "velvetg" fails in all three cases. Thus, the problem is that VelvetOptimiser is not able to locate/execute the velvetg executable. As a consequence, there is of course no stats.txt as it is usually generated by velvetg.

Possible solutions:
1. Check the permissions of velvetg, maybe your Script is not allowed to run it.

ls -al `which velvetg`

2. Find out, whether your velvetg executable is in the PATH (if not the above might not have worked either.)by running

velvetg

If it doesn't run, you might want to reinstall velvet, correctly.

Disclaimer: I have never used the VelvetOptimiser script and just try to help you find the source of the problem

Thank for help, i have just reinstall ubtuntu 13.10 and still problem while using velvetoptimiser
This problem is:
Use of uninitialized value in numeric ne (!=) at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value in numeric gt (>) at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Th10 23 09:58:53 Hash value of best assembly by assembly score: 31
Th10 23 09:58:53 Optimisation routine chosen for best assembly: shortPaired
Th10 23 09:58:53 Looking for the expected coverage
Unable to open /home/tnt/auto_data_31/stats.txt for exp_cov determination.
at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 838
Can you help me?

[Votinhkiem90]

Thank for help, i have just reinstall ubtuntu 13.10 and still problem while using velvetoptimiser
This problem is:
Use of uninitialized value in numeric ne (!=) at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value in numeric gt (>) at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Th10 23 09:58:53 Hash value of best assembly by assembly score: 31
Th10 23 09:58:53 Optimisation routine chosen for best assembly: shortPaired
Th10 23 09:58:53 Looking for the expected coverage
Unable to open /home/tnt/auto_data_31/stats.txt for exp_cov determination.
at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 838
Can you help me?

i have fixed this problem, thanks for your help.

[leirhyh]

the simillar errors, how to fix it.

Hi, Votinhkiem90:
I'm glad that you fixed that errors.

When I run VelvetOptimiser.pl, I meet the same errors as follows:
Use of uninitialized value in numeric ne (!=) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value $maxScore in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric ne (!=) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value $maxScore in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Apr 4 18:11:16 Hash value of best assembly by assembly score: 83
Apr 4 18:11:16 Optimisation routine chosen for best assembly: shortPaired
Apr 4 18:11:16 Looking for the expected coverage
Unable to open /media/Athena/radiated/trimmeddata/auto_data_83/stats.txt for exp_cov determination.
at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 838

I checked botth Velveth and Velvetg, which works fine for this PATH.

Could you give me some hints on how to fix this?

Thank you very much and I appreciate your time.

[Votinhkiem90]

Hi, Votinhkiem90:
I'm glad that you fixed that errors.

When I run VelvetOptimiser.pl, I meet the same errors as follows:
Use of uninitialized value in numeric ne (!=) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value $maxScore in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric ne (!=) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value $maxScore in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Apr 4 18:11:16 Hash value of best assembly by assembly score: 83
Apr 4 18:11:16 Optimisation routine chosen for best assembly: shortPaired
Apr 4 18:11:16 Looking for the expected coverage
Unable to open /media/Athena/radiated/trimmeddata/auto_data_83/stats.txt for exp_cov determination.
at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 838

I checked botth Velveth and Velvetg, which works fine for this PATH.

Could you give me some hints on how to fix this?

Thank you very much and I appreciate your time.

Yes, Possible you wrong for parameters cause this error. However You should check VelvetOptimiser install, and retype right parameters.
Good luck
p/s: can you sent the parameter that you run.

[leirhyh]

about running VelvetOptimiser.pl

Hi,Votinhkiem90:
My running conndition is as follows:
/software/VelvetOptimiser/VelvetOptimiser.pl -s 19 -e 99 -f '-shortPaired -fastq lava8.2ta1.fastq lava8.2ta2.fastq'

What do you think?

Thanks,

All the best,

Runhua

Originally Posted by leirhyh View Post
Hi, Votinhkiem90:
I'm glad that you fixed that errors.

When I run VelvetOptimiser.pl, I meet the same errors as follows:
Use of uninitialized value in numeric ne (!=) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value $maxScore in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric ne (!=) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value $maxScore in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Use of uninitialized value in numeric gt (>) at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Apr 4 18:11:16 Hash value of best assembly by assembly score: 83
Apr 4 18:11:16 Optimisation routine chosen for best assembly: shortPaired
Apr 4 18:11:16 Looking for the expected coverage
Unable to open /media/Athena/radiated/trimmeddata/auto_data_83/stats.txt for exp_cov determination.
at /software/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 838

I checked botth Velveth and Velvetg, which works fine for this PATH.

Could you give me some hints on how to fix this?

Thank you very much and I appreciate your time.
Yes, Possible you wrong for parameters cause this error. However You should check VelvetOptimiser install, and retype right parameters.
Good luck
p/s: can you sent the parameter that you run.

[paa6]

Thank for help, i have just reinstall ubtuntu 13.10 and still problem while using velvetoptimiser
This problem is:
Use of uninitialized value in numeric ne (!=) at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
Use of uninitialized value in numeric gt (>) at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
Th10 23 09:58:53 Hash value of best assembly by assembly score: 31
Th10 23 09:58:53 Optimisation routine chosen for best assembly: shortPaired
Th10 23 09:58:53 Looking for the expected coverage
Unable to open /home/tnt/auto_data_31/stats.txt for exp_cov determination.
at Downloads/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 838
Can you help me?

I have also used velvetoptimiser recently but unable to understand result...can u please give me some hints how to start....I would really appreciate ur time...

[Votinhkiem90]

I have also used velvetoptimiser recently but unable to understand result...can u please give me some hints how to start....I would really appreciate ur time...

You have been run step by step with velvet with defaults parameters yet?
I think you should test with velvet before run with VelvetOpt. Now I don't use VelvetOptimiser along time ago, so im not sure how to fix this problem. but I guess this error from you cmd and parameter that you run.

[paa6]

You have been run step by step with velvet with defaults parameters yet?
I think you should test with velvet before run with VelvetOpt. Now I don't use VelvetOptimiser along time ago, so im not sure how to fix this problem. but I guess this error from you cmd and parameter that you run.

I did try velvet before but now I am using velvetoptimiser. It's all that I am unable to understand results properly because there is no clear explanation for that..so can u give me some links for result analysis.