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Old 02-05-2017, 01:19 PM   #1
PryceMichener
Junior Member
 
Location: Memphis, TN

Join Date: Sep 2015
Posts: 2
Default Velvetg not producing output files through Velvetoptimiser

I am running VelvetOptimiser, and the code works through velveth and velvetg, but velvetg does not produce any of the output files that its supposed to. I don't have the stats.txt file in the output directories, meaning that VelvetOptimiser won't continue. My log files are below, does anyone have any idea what's wrong?

Here's my code:
Code:
perl ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl -s 51 -e 71 -p Verr_rein -o 'Verr_rein_Velv -ins_length 350 -exp_cov auto -cov_cutoff auto' -f '-fasta -shortPaired ./Output/Verreauxia_reinwardtii_823.together_paired.fasta -fasta -short ./Output/Verreauxia_reinwardtii_823.together_singletons.fasta'
Here is an excerpt from the assembly log file. This is the last assembly and then the final messages:

Code:
> Assembly id: 11
> 
> Velveth timestamp: Nov 29 2016 16:36:08
> 
> Velvetg timestamp: Nov 29 2016 16:36:30
> 
> Velveth version: 1.2.10
> 
> Velvetg version: 1.2.10
> 
> Readfile(s): -fasta -shortPaired
> ./Output/Verreauxia_reinwardtii_823.together_paired.fasta -fasta
> -short 
> 
> ./Output/Verreauxia_reinwardtii_823.together_singletons.fasta
> 
> Velveth parameter string: Verr_rein_data_71 71 -fasta -shortPaired 
> 
> ./Output/Verreauxia_reinwardtii_823.together_paired.fasta -fasta
> -short 
> 
> ./Output/Verreauxia_reinwardtii_823.together_singletons.fasta
> 
> Velvetg parameter string: Verr_rein_data_71 Verr_rein_Velv -ins_length
> 350 -exp_cov auto -cov_cutoff auto -clean yes
> 
> Assembly directory: /a/b/c/reads/Verr_rein_data_71
> 
> Velvet hash value: 71
> 
> Roadmap file size: 932222
> 
> Paired Library insert stats:
> 
> **********************************************************
> 
> Nov 29 16:36:32 Best assembly by assembly score - assembly id: 6
> 
> Nov 29 16:36:32 Optimisation routine chosen for best assembly:
> shortPaired
> 
> Nov 29 16:36:32 Looking for the expected coverage
And here's the output from VelvetOptimiser:

Code:
> Velvet details:
> 
>         Velvet version: 1.2.10
> 
>         Compiled categories: 2
> 
>         Compiled max kmer length: 99
> 
>         Maximum number of velvetinstances to run: 32
> 
> Will run velvet optimiser with the following paramters:
> 
>         Velveth parameter string:
> 
>                 -fasta -shortPaired ./Output/Verreauxia_reinwardtii_823.together_paired.fasta -fasta
> -short  ./Output/Verreauxia_reinwardtii_823.together_singl
> 
> etons.fasta
> 
>         Velveth start hash values:      51
> 
>         Velveth end hash value:         71
> 
>         Velveth hash step value:        2
> 
>         Velvetg minimum coverage cutoff to use: 0
> 
>         Read tracking for final assembly off.
> 
> Nov 29 16:35:47 Beginning velveth runs.
> 
> Nov 29 16:35:47         Running velveth with hash value: 51.
> 
> Nov 29 16:35:48         Velveth with hash value 51 finished.
> 
> Nov 29 16:35:49         Running velveth with hash value: 53.
> 
> Nov 29 16:35:51         Velveth with hash value 53 finished.
> 
> Nov 29 16:35:51         Running velveth with hash value: 55.
> 
> Nov 29 16:35:53         Velveth with hash value 55 finished.
> 
> Nov 29 16:35:53         Running velveth with hash value: 57.
> 
> Nov 29 16:35:54         Velveth with hash value 57 finished.
> 
> Nov 29 16:35:55         Running velveth with hash value: 59.
> 
> Nov 29 16:35:57         Velveth with hash value 59 finished.
> 
> Nov 29 16:35:57         Running velveth with hash value: 61.
> 
> Nov 29 16:35:58         Velveth with hash value 61 finished.
> 
> Nov 29 16:35:59         Running velveth with hash value: 63.
> 
> Nov 29 16:36:01         Velveth with hash value 63 finished.
> 
> Nov 29 16:36:01         Running velveth with hash value: 65.
> 
> Nov 29 16:36:03         Velveth with hash value 65 finished.
> 
> Nov 29 16:36:03         Running velveth with hash value: 67.
> 
> Nov 29 16:36:04         Velveth with hash value 67 finished.
> 
> Nov 29 16:36:05         Running velveth with hash value: 69.
> 
> Nov 29 16:36:06         Velveth with hash value 69 finished.
> 
> Nov 29 16:36:07         Running velveth with hash value: 71.
> 
> Nov 29 16:36:08         Velveth with hash value 71 finished.
> 
> Nov 29 16:36:09 Finished velveth runs.
> 
> Nov 29 16:36:09 Beginning vanilla velvetg runs.
> 
> Nov 29 16:36:09         Running vanilla velvetg on hash value: 51
> 
> Nov 29 16:36:09         Velvetg on hash value: 51 finished.
> 
> Nov 29 16:36:11         Running vanilla velvetg on hash value: 53
> 
> Nov 29 16:36:11         Velvetg on hash value: 53 finished.
> 
> Nov 29 16:36:13         Running vanilla velvetg on hash value: 55
> 
> Nov 29 16:36:13         Velvetg on hash value: 55 finished.
> 
> Nov 29 16:36:16         Running vanilla velvetg on hash value: 57
> 
> Nov 29 16:36:16         Velvetg on hash value: 57 finished.
> 
> Nov 29 16:36:18         Running vanilla velvetg on hash value: 59
> 
> Nov 29 16:36:18         Velvetg on hash value: 59 finished.
> 
> Nov 29 16:36:20         Running vanilla velvetg on hash value: 61
> 
> Nov 29 16:36:20         Velvetg on hash value: 61 finished.
> 
> Nov 29 16:36:22         Running vanilla velvetg on hash value: 63
> 
> Nov 29 16:36:22         Velvetg on hash value: 63 finished.
> 
> Nov 29 16:36:24         Running vanilla velvetg on hash value: 65
> 
> Nov 29 16:36:24         Velvetg on hash value: 65 finished.
> 
> Nov 29 16:36:26         Running vanilla velvetg on hash value: 67
> 
> Nov 29 16:36:26         Velvetg on hash value: 67 finished.
> 
> Nov 29 16:36:28         Running vanilla velvetg on hash value: 69
> 
> Nov 29 16:36:28         Velvetg on hash value: 69 finished.
> 
> Nov 29 16:36:30         Running vanilla velvetg on hash value: 71
> 
> Nov 29 16:36:30         Velvetg on hash value: 71 finished.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Use of uninitialized value in numeric ne (!=) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 289.
> 
> Use of uninitialized value $maxScore in numeric gt (>) at
> ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 290.
> 
> Nov 29 16:36:32 Hash value of best assembly by assembly score: 61
> 
> Nov 29 16:36:32 Optimisation routine chosen for best assembly:
> shortPaired
> 
> Nov 29 16:36:32 Looking for the expected coverage
> 
> Unable to open /a/b/c/reads/Verr_rein_data_61/stats.txt
> for exp_cov determination.
> 
>  at ./programs/VelvetOptimiser-2.2.5/VelvetOptimiser.pl line 838.

Thanks in advance!
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Old 02-06-2017, 04:45 PM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default

I can't remember if I've ever used VelvetOptimiser, so I'm not familiar with its output. Have you tried running velveth and velvetg, without VelvetOptimiser, for just one of the kmer sizes, to see whether velvetg produces all the output files or if it has problems?
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