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:
Here is an excerpt from the assembly log file. This is the last assembly and then the final messages:
And here's the output from VelvetOptimiser:
Thanks in advance!
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'
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
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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