Question: Velvetg not producing output files
0
gravatar for Pryce Michener
2.4 years ago by
Memphis, TN
Pryce Michener10 wrote:

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 is an excerpt from the assembly log file. This is the last assembly and then the final messages:

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:

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!

velvet velvetg • 1.0k views
ADD COMMENTlink modified 2.4 years ago by k.kathirvel93190 • written 2.4 years ago by Pryce Michener10

Hi Pryce - did you have any luck solving this issue? I'm having the same problem and can't seem to find a solution.

ADD REPLYlink written 2.1 years ago by baroquemon0
1
gravatar for k.kathirvel93
2.4 years ago by
k.kathirvel93190
India
k.kathirvel93190 wrote:

./velvetOptimiser.pl -s 51 -e 71 -f '-shortPaired -Separate -fastq input1 input2 --OptFuncKmer 'n50'

Try this for paired-end...

From this also you cannot find a solution.....Pls go for a Velvet-stats, which is very easier than velvetoptimiser...Thanks

ADD COMMENTlink written 2.4 years ago by k.kathirvel93190
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