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GATB / simka

Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
https://gatb.inria.fr/software/simka/
GNU Affero General Public License v3.0
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Fails to run #2

Open raw937 opened 7 years ago

raw937 commented 7 years ago

lala [0.0%] Computing k-mer spectrums [Time: 0:00:00]A job failed (simka_test_tmp/simka_database/kmer_spectrums/A/), exiting simka

raw937 commented 7 years ago

used a cmake/3.3.0 and gcc/6.1.0 to install.

rchikhi commented 7 years ago

command line?

raw937 commented 7 years ago

python scripts/simka2/simka.py -in example/data/simka_input.txt -kmer-size 4 -abundance-min 10 -out simka_test -out-tmp simka_test_tmp

On Fri, Mar 3, 2017 at 4:22 PM, Rayan Chikhi notifications@github.com wrote:

command line?

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raw937 commented 7 years ago

?

rchikhi commented 7 years ago

thanks for the command-line. I don't see what's wrong with it, except maybe quite small k-mer sizes. (possibly outside the range of tested kmer sizes) I'll let simka's developers investigate and reply to this one.. Meanwhile could you please report whether the command worked with larger kmer size? e.g. 10

michoug commented 7 years ago

Hi, I have the same issue installing from source, so version 2,0 However it works fine with version 1.3.2 installing with the release version Best Greg

GatouResearch commented 7 years ago

Hi, This command works fine for me on mac and linux. Can you send me the output of the failing job with the following command: cat simka_test_tmp/simka_database/kmer_spectrums/A/log.txt

michoug commented 7 years ago

Hi, here is the output for my issue

lala
[0.0%] Computing k-mer spectrums    [Time: 0:00:00]A job failed (simka_temp/simka_database/kmer_spectrums/BODY/), exiting simka
python /home/michoug/simka/scripts/simka2/core/simka2-run-job.py simka_temp/simka_database/kmer_spectrums/BODY/ count /home/michoug/simka/scripts/simka2/core/../bin/simka2-count -id BODY -in simka_temp/simka_tmp/BODY_temp/input.txt -out-tmp simka_temp/simka_tmp/BODY_temp -out simka_temp/simka_database/kmer_spectrums/BODY -kmer-size 21 -max-reads 10000000 -min-read-size 0 -read-shannon-index 0 -nb-dataset 2 -abundance-min 2 -abundance-max 2147483647 -nb-partitions 5 -max-memory 50000 -nb-cores 2

[DSK: Pass 1/1, Step 1: partitioning     ]  0    %   elapsed:   0 min 0  sec   remaining:   0 min 0  sec   cpu:  -1.0 %   mem: [   8,    8,    8] MB Segmentation fault (core dumped)
[DSK: Pass 1/1, Step 1: partitioning     ]  0    %   elapsed:   0 min 0  sec   remaining:   0 min 0  sec   cpu:  -1.0 %   mem: [   8,    8,    8] MB Segmentation fault (core dumped)
[DSK: Pass 1/1, Step 1: partitioning     ]  0    %   elapsed:   0 min 0  sec   remaining:   0 min 0  sec   cpu:  -1.0 %   mem: [   8,    8,    8] MB Segmentation fault (core dumped)

------
['/home/michoug/simka/scripts/simka2/core/simka2-run-job.py', 'simka_temp/simka_database/kmer_spectrums/BODY/', 'count', '/home/michoug/simka/scripts/simka2/core/../bin/simka2-count', '-id', 'BODY', '-in', 'simka_temp/simka_tmp/BODY_temp/input.txt', '-out-tmp', 'simka_temp/simka_tmp/BODY_temp', '-out', 'simka_temp/simka_database/kmer_spectrums/BODY', '-kmer-size', '21', '-max-reads', '10000000', '-min-read-size', '0', '-read-shannon-index', '0', '-nb-dataset', '2', '-abundance-min', '2', '-abundance-max', '2147483647', '-nb-partitions', '5', '-max-memory', '50000', '-nb-cores', '2']

------
/home/michoug/simka/scripts/simka2/core/../bin/simka2-count -id BODY -in simka_temp/simka_tmp/BODY_temp/input.txt -out-tmp simka_temp/simka_tmp/BODY_temp -out simka_temp/simka_database/kmer_spectrums/BODY -kmer-size 21 -max-reads 10000000 -min-read-size 0 -read-shannon-index 0 -nb-dataset 2 -abundance-min 2 -abundance-max 2147483647 -nb-partitions 5 -max-memory 50000 -nb-cores 2 

Exec
/home/michoug/simka/scripts/simka2/core/../bin/simka2-count -id BODY -in simka_temp/simka_tmp/BODY_temp/input.txt -out-tmp simka_temp/simka_tmp/BODY_temp -out simka_temp/simka_database/kmer_spectrums/BODY -kmer-size 21 -max-reads 10000000 -min-read-size 0 -read-shannon-index 0 -nb-dataset 2 -abundance-min 2 -abundance-max 2147483647 -nb-partitions 5 -max-memory 50000 -nb-cores 2 
Ret: 35584
Nb try: 1

Exec
/home/michoug/simka/scripts/simka2/core/../bin/simka2-count -id BODY -in simka_temp/simka_tmp/BODY_temp/input.txt -out-tmp simka_temp/simka_tmp/BODY_temp -out simka_temp/simka_database/kmer_spectrums/BODY -kmer-size 21 -max-reads 10000000 -min-read-size 0 -read-shannon-index 0 -nb-dataset 2 -abundance-min 2 -abundance-max 2147483647 -nb-partitions 5 -max-memory 50000 -nb-cores 2 
Ret: 35584
Nb try: 2

Exec
/home/michoug/simka/scripts/simka2/core/../bin/simka2-count -id BODY -in simka_temp/simka_tmp/BODY_temp/input.txt -out-tmp simka_temp/simka_tmp/BODY_temp -out simka_temp/simka_database/kmer_spectrums/BODY -kmer-size 21 -max-reads 10000000 -min-read-size 0 -read-shannon-index 0 -nb-dataset 2 -abundance-min 2 -abundance-max 2147483647 -nb-partitions 5 -max-memory 50000 -nb-cores 2 
Ret: 35584
End: 35584
GatouResearch commented 7 years ago

Ok, unfortunatelly I won't be able to solve this issue without running simka myself with your dataset. Is "BODY" dataset a public dataset ?

michoug commented 7 years ago

Unfortunately no, As of now, the version 1.3.2 works so I'll continue with it. If I have the same issue with a public dataset, I'll send it to you

aponsero commented 7 years ago

Hi! Sorry to bother you. But I do have the same trouble. When I run the toy exemple line : python ./scripts/simka2/simka.py -in ./example/data/simka_input.txt -out simka_results -out-tmp simka_temp

I get :

lala [0.0%] Computing k-mer spectrums [Time: 0:00:00]A job failed (simka_temp/simka_database/kmer_spectrums/A/), exiting simka

And when I installed it, I noticed it sent an error (error_installing_SIMKA.txt ) I installed it using : 

git clone https://github.com/GATB/simka.git
cd simka
sh INSTALL
GatouResearch commented 7 years ago

Hi Oh yes you have an install issue, can I know what are your cmake and gcc versions ? you can get them by typing "cmake --version" and "gcc --version"

aponsero commented 7 years ago

Thank you so much for your rapid answer ! Because of previous comments on this thread, I tried the installation of the previous release (V1.3.2), and it also fails.

cmake version 2.8.12.2 gcc (GCC) 5.2.0

Also, I got the same error when installing on another HPC cluster (same cmake version, gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17) )

aponsero commented 7 years ago

Hi again, After multiple trials, I managed to have a complete installation on a ubuntu VM with the following settings : gcc 4.9.4 cmake 2.8.12.2

no other version of gcc worked for me...

However, the toy example still fails. and in the /simka/simka_temp/simka_database/kmer_spectrums/A folder , the log.txt reveal a problem with the kmer spectrum log.txt

What can I do ?

GatouResearch commented 7 years ago

Hi,

thanks for your feedback,
unfortunately at the moment, I have no ideas how to fix those issues...

You can also try precompiled binaries in the release tab: https://github.com/GATB/simka/releases/tag/v1.3.2 There are for linux (bin-Linux) and mac (bin-darwin).

GatouResearch commented 7 years ago

Hi everyone,

I have released a new version of Simka v1.4 : https://github.com/GATB/simka/releases/tag/v1.4.0 It should fix a lot of compilation issues and integrate new functionalities.

I hope it's going to fix this issue.