comprna/RATTLE

No output file generated!!!

Amrita-Vijay opened this issue · 14 comments

Amrita-Vijay commented

Hi,

I am trying to run the rattle cluster for my nanopore data and even after the run is complete there is no output file generated.

could you please help me with this.

Thanks!

EduEyras commented
Amrita-Vijay commented
novikk commented

Hi,
this is because in the command line you specified "/IH2" as the output folder, which is a folder starting from the root of your system, and not in the current folder.

If you do "cd /IH2" and that folder exists, the output should be there.

If you want to save it in the current folder, then the path shouldn't start with "/", and you should first create the folder, like this:

mkdir IH2
./RATTLE/rattle cluster -i IH-BP01_10k.fq.gz -o IH2 -t 36 --fastq

Tell me if that worked for you!
Ivan

Amrita-Vijay commented

Hi,

I tried and It didn't work for me.

yeroslaviz commented

Did you manage to solve the problem?
I also have two runs, which finished with no errors, but the output folders are empty

mkdir  -p Analysis/Nanopore_06.2022/rattle/
$rattle cluster --input $FAT11673 --output Analysis/Nanopore_06.2022/rattle/ --threads 15 --kmer-size 12 --verbose --rna

No ideas, where the output can be or if it was created at all.

Amrita-Vijay commented
eileen-xue commented

Hi @yeroslaviz,

Can you please provide us with the output lines of your run? Does it print the reads numbers, cluster numbers or throw any error messages?

Thanks,
Eileen

yeroslaviz commented

Yes. I was able to resolve this
…
________________________________ From: yeroslaviz @.> Sent: 19 August 2022 16:23 To: comprna/RATTLE @.> Cc: Amrita Vijay @.>; Author @.> Subject: Re: [comprna/RATTLE] No output file generated!!! (#24) ...

can you elaborate on that?
how?

yeroslaviz commented

This is my complete output.

$ $rattle cluster --input $FAT11673 --output Analysis/Nanopore_06.2022/rattle/ --threads 15 --kmer-size 12 --verbose --rna
RNA mode: true
Reading fasta file... Done
[>                                                                               ] 83/2308867 (0.00359484%))
[================================================================================] 2308867/2308867 (100%)99%)
[================================================================================] 172413/172413 (100%)94%)
Iteration 0.35 complete
[================================================================================] 91162/91162 (100%)89%)
Iteration 0.3 complete
[================================================================================] 60147/60147 (100%)83%)
Iteration 0.25 complete
[================================================================================] 44727/44727 (100%)78%)
Iteration 0.2 complete
[================================================================================] 35167/35167 (100%)72%)
Iteration 0 complete
Gene clustering done
24140 gene clusters found
eileen-xue commented

It seems that you are not using the latest version. Please update it because the new version has an output folder path check.

Also, please check and ensure you have the write permission of the output folder.

Please let me know whether this helps.

Thanks,
Eileen

yeroslaviz commented

I deleted the RATTLE folder, and downloaded it again.

I did as followed

git clone --recurse-submodules https://github.com/comprna/RATTLE
cd RATTLE
./build.sh

which gave me the following error:

g++ -o rattle -Wall -Wextra -std=c++14 -O3 -pthread -Ispoa/include main.cpp fasta.o -lz cluster.o utils.o kmer.o similarity.o correct.o spoa/build/lib/libspoa.a
g++: error: spoa/build/lib/libspoa.a: No such file or directory
make: *** [Makefile:9: rattle] Error 1
eileen-xue commented

This error means you haven't fully downloaded RATTLE repository. Try to download it again, or just download the submodules hps and spoa two folders. If those two folders are empty, RATTLE cannot be installed successfully and won't be able to generate output files in cluster step.

Please check your git version. If your git version is before 2.13, you may need to use --recursive to replace --recurse-submodules to download the submodules.

Thanks,
Eileen

yeroslaviz commented

Ok, I managed to install rattle now.

Now I ran it first without the output folder to see the changes. this works. I created the folder and checked for permissions. Now I run it with the complete command.

$rattle cluster --input $FAR52442 --output Analysis/Nanopore_04.2022/rattle/ --threads 36 --kmer-size 12 --verbose --rna

Output folder doesn't exit. Please create it first.
$ mkdir -p Analysis/Nanopore_04.2022/rattle/
$ ll  Analysis/Nanopore_04.2022/rattle/
total 2
drwxr-xr-x 2 yeroslaviz b_cox 4096 Aug 19 11:13 ./
drwxr-xr-x 9 yeroslaviz b_cox 4096 Aug 19 11:13 ../
$rattle cluster --input $FAR52442 --output Analysis/Nanopore_04.2022/rattle/ --threads 36 --kmer-size 12 --verbose --rna
RNA mode: true
Reading fasta file...
Reads: 12246248

...

I update, when the run is done

my git version is 2.34

Thanks for the help.

yeroslaviz commented

Just wanted to let you know, that i now have the output file. thanks again