Entering edit mode
10.1 years ago
Anaïs Vittu
•
0
Hello,
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)'
[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 !
Anaïs
Ok, there are very similar!
The first character is a "@" and not a ">", that's why I think.
Thanks for the follow-up, this is strange, can you please paste the output of the commands
uname -aandcat /etc/*-release?The version of KmerGenie that I am using is 1.6741.
Thanks. Please give me some time, I'll try on a Mac machine to see if I can somehow reproduce the problem.
Hello,
I try on a Linux machine.
And it did not work. It saw 3 files in my file but there are only 2.
I tried the fastq file directly and it worked !
I really do not understand why.
I used kmergenie version 1.5579.
Nice that you have a Linux machine handy. Regarding that problem, it seems that you have 3 lines in the .txt file, one of them is empty I suppose? If so, that's the problem. Could it be that your shell adds an empty line after each command automatically?
Regardless, I'll work on input cleaning of .txt files.
Indeed, there was a "\n" in the third line. I removed it and Kmergenie worked well.
But it is on a Linux machine and it is the version 1.5579. I will install the last version 1.6741 to try.
Otherwise, I check something else on my Mac :
Ok, so when I change the name of my input file, it works. But not all changes worked (example toto).
And when I create the file with the names of my 2 fastq files changed, it did not work. I obtained the same results with the version 1.5579.