vmatch related error

[ShaolinXU]

Hello,

I'm trying to use SRAssembler to assemble a mitochondria genomee.
I'm using singularity to run SRAssembler_MPI, and provided a DNA seed sequence
The pre-processing is finished properly. However, there seem like something wrong with vmatch at the first round, the error massage is vmatch: searchlength=8 must be >= 12=prefixlen.
I have followed your tutorial, and made sure that the vmatch setup is fine in my case. here are how I set the vmatch parameters:

[Vmatch_dna_init]       
l=35                    
e=3                     
[Vmatch_extend_contig]  
l=25                    
e=0

could you please give me some suggestion about how to debug my command.
All the best

---

bellow are the log file that I made, could be useful.

[2020-06-16 08:45:24] [INFO] SRAssembler v1.0.0 command: SRAssembler_MPI -q chydriae_sp_COI.fasta -t dna -p SRAssembler.conf -l library_file -M 16000 -R 2000000
[2020-06-16 08:45:24] [INFO] Total processors: 8
[2020-06-16 08:45:24] [INFO] We have 1 libraries
[2020-06-16 08:45:24] [INFO] library 1: Italy_sample
[2020-06-16 08:45:24] [INFO] insert size: 350
[2020-06-16 08:45:24] [INFO] left read: Italy_sample_R1.fq
[2020-06-16 08:45:24] [INFO] right read: Italy_sample_R2.fq
[2020-06-16 08:45:24] [INFO] reversed: 0
[2020-06-16 08:45:24] [INFO] Paired-end: 1
[2020-06-16 08:45:24][DOING] Now pre-processing the reads files ...
[2020-06-16 08:45:24] [INFO] Using previously split files for read library 1
[2020-06-16 08:45:24][DOING] Preprocessing done.
[2020-06-16 08:45:24] [INFO] Begin chromosome walking ...
[2020-06-16 08:45:24] [INFO] Starting round 1 ...
[2020-06-16 08:45:24][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 2 of 22
[2020-06-16 08:45:24][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 1 of 22
[2020-06-16 08:45:24][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 3 of 22
[2020-06-16 08:45:24][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 4 of 22
[2020-06-16 08:45:24][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 5 of 22
[2020-06-16 08:45:24][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 6 of 22
[2020-06-16 08:45:24][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 7 of 22
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 8 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 14 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 9 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 13 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 10 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 12 of 22
vmatch: searchlength=8 must be >= 12=prefixlen
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 11 of 22
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 21 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 16 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 20 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 15 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 19 of 22
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 18 of 22
vmatch: searchlength=8 must be >= 12=prefixlen
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 17 of 22
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
[2020-06-16 08:45:25][DOING] Aligning using Vmatch criteria dna_init: Round 1, Lib 1 of 1, Reads chunk 22 of 22
vmatch: searchlength=8 must be >= 12=prefixlen
vmatch: searchlength=8 must be >= 12=prefixlen
[2020-06-16 08:45:25] [INFO] The walking is terminated: No new reads found.
[2020-06-16 08:45:25][DOING] Checking the final contigs assembled in round 1 ...
[2020-06-16 08:45:25] [INFO] ... no contigs found in round 1
[2020-06-16 08:45:25] [INFO] Execution time: 1 seconds

[vpbrendel]

1. Unrelated to the error, but the argument to -R is probably not what you want. Please see what -R is about.

2. Your criteria are l=35 e=3; i.e., with maximal spacing of errors you could have 8M E 8M E 8M E 8M for a match of length 35 with four blocks of 8 matches (M) and 3 errors (E) interspersed..

3. Your read space seems to be huge, so vmatch suggests using 12-mers rather than 8-mers for a first hit. So, maybe what you want is to capture 12M E 12M E 12M E 12M, i.e. use criteria

l=51
e=3

in the Vmatch_dna_init paragraph?

[Wyinghao]

Hello！
I encountered the same problem. May I ask you some questions regarding vmatch? I received an error while using vmatch: vmatch: searchlength=9 must be >= 11=prefixlen.
This is my command:
1.mkvtree -db Merged.LTR.Up_Down.Chr.fa -dna -pl -allout -v2.vmatch -dbcluster 70 70 -p -d -l 200 -identity 80 -showdesc 0 -e 20 Merged.LTR.Up_Down.Chr.fa > Merged.LTR.Chr.count