I am trying to run kmergenie on paired-end reads. So I created a file with the 2 files and ran kmergenie like below.
anais$ ls -l *.fq -rw-r--r-- 1 anais staff 326796250 22 oct 11:58 C0CYDACXX_1.fq -rw-r--r-- 1 anais staff 326796250 22 oct 11:58 C0CYDACXX_2.fq
anais$ ls -l *.fq > filesToAssemble.txt
anais$ kmergenie filesToAssemble.txt running histogram estimation File filesToAssemble.txt starts with character "f", hence is interpreted as a list of file names Reading 0 read files fitting model to histograms to estimate best k could not predict a best k value Execution of decide failed (return code 0)
Kmergenie interpreted my input as a file, right but after it was not able to read the 2 files.
So I decided to input directly 1 fastq file and it did not recognize it as a fastq file.
anais$ kmergenie C0CYDACXX_1.fq running histogram estimation File C0CYDACXX_1.fq starts with character "C", hence is interpreted as a list of file names Reading 0 read files fitting model to histograms to estimate best k could not predict a best k value Execution of decide failed (return code 0)
Anyone have a suggestion on what is going on ?
The make check was successful.
anais$ make check scripts/test_install Testing presence of specialk.... OK Testing presence of Rscript.... R scripting front-end version 2.15.1 (2012-06-22) OK Testing basic Rscript functionality.... Rscript --no-init-file -e 'rnorm(1)'  "rnorm(1)" OK Testing a simple KmerGenie example.... initial estimate of genomic kmers gaussian mean, sd, error proportion, shape: 3 1.4826 0.9596929 0 p$u.v: 4.114784 abundance ratio_of_erroneous_over_correct_kmers 1 23228317 2 0.000002223243 3 0.000000007846881 4 0.0000000008400604 cutoff: 1 sum probs good 1.001097cutoff 1 non-repeated genomic distinct kmers: 42 repeated genomic distinct kmers: 0 sum of absolute differences of fit: 2.145231 42 Test successful if the number 42 was printed the line above. KmerGenie is ready, type `./kmergenie`.
Thank you for helping me !