vpbrendel
commented
4 years ago 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?
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: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