Hi
I have installed metassembler and the testdatset runs through smoothly
Now I tried to run it on two genome assemblies using the config file below but keep getting this error
sys.exit('ERROR: Not enough information to compute CE-stat for %s.\nread1=%s\nread2=%s\nmaxins=%s\nminins=%s\n' %(read1,read2,maxins,minins))
TypeError: not enough arguments for format string
ALl used pathes are fine, input files are also fine (fastq files are correct), I checked the parameters for the config file in the manual and I cant find what I am missing here
All dependencies work fine as well since the test dataset went through without any issues.
I solved the proble, metassemble needs a value bigger than 0 for bowtie2_minins (apparetntly) whereas the bowtie2 manual page says 0 is default
-I/--minins <int>
"The minimum fragment length for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates.
The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences between -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.
Default: 0 (essentially imposing no minimum)"
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Hi
I have installed metassembler and the testdatset runs through smoothly
Now I tried to run it on two genome assemblies using the config file below but keep getting this error
sys.exit('ERROR: Not enough information to compute CE-stat for %s.\nread1=%s\nread2=%s\nmaxins=%s\nminins=%s\n' %(read1,read2,maxins,minins))
TypeError: not enough arguments for format string
ALl used pathes are fine, input files are also fine (fastq files are correct), I checked the parameters for the config file in the manual and I cant find what I am missing here
All dependencies work fine as well since the test dataset went through without any issues.
Metassemble configuration file suggested template
[global]
Mate-pair mapping parameters:
bowtie2_threads=8
bowtie2_read1=all_1P.fastq
bowtie2_read2=all_2P.fastq
bowtie2_maxins=1000
bowtie2_minins=0
genomeLength=950000000
meta2fasta_keepUnaligned=3
meta2fasta_sizeUnaligned=350 350
nucmer_l=50
nucmer_c=300
CE-stat computation parameters:
mateAn_s=500
mateAn_m=350
[1]
fasta=celera/all_females.scf.fasta
ID=CeleraFemales
mateAn_file=
[2]
fasta=/spades/scaffolds.fasta
ID=SpadesFemales
mateAn_file=
I solved the proble, metassemble needs a value bigger than 0 for bowtie2_minins (apparetntly) whereas the bowtie2 manual page says 0 is default
-I/--minins <int>
"The minimum fragment length for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates.
The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences between -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.
Default: 0 (essentially imposing no minimum)"