culebrONT test run giving error!

[aswathyseb]

Hi,

Thank you for this pipeline. I am testing out using the test dataset on a local machine.

The command I ran is

culebrONT run_local -t 8 -c test/data_test_config.yaml

But I get this error

Error in rule run_canu: jobid: 7 ERROR: Invalid command line option '/home/aswathy/tmp/test/Data-Xoo-sub/fastq/5percentB1-1.fastq.gz'. Did you forget quotes around options with spaces?

Attached is the detailed error message.

error.txt

Could you please help me resolve this?

Thank you

[sravel]

Hello Thanks for use CulebrONT !!! Could you please send us complet log file? we need to ckeck the snakemake command line to help you

However, we think you need to binding singularity: see https://sylabs.io/guides/3.0/user-guide/bind_paths_and_mounts.html

you have 2 solutions to bind singularity:

• directly on the culebront command line culebrONT run_local -t 8 -c test/data_test_config.yaml --singularity-args "--bind $HOME"
• or declaring a singularity global variable in your system, doing a export SINGULARITY_BIND="/home:/home" in your ~/.bashrc

We wait for your news !

Thanks,

[aswathyseb]

Binding singularity solved the issue. I was able to run it.

Thank you.

[aswathyseb]

Hello,

Unfortunately when I try on my dataset I get the error that my fastq file doen't exist when it is actually present in the folder. The command I ran is

time culebrONT run_local -c config.yaml -t 15 --singularity-args "--bind $HOME"

Attached are the log files and the config file

snakemake.log

config.yaml.txt

ccs_MINIASM.e.txt

Could you please help?

[sravel]

Hello Can you write the snakemake command line in the log file? Is it the good path? /analysis/work/aswathy/projects/scott-linder/pacbio_assembly_pyoelii/trials/culebrONT/data/fastq/ccs.fq

because when you write relative path on config.yaml the absolute path is build relative to the file: so for you i think is like this:

/analysis/work/aswathy/projects/scott-linder/pacbio_assembly_pyoelii/trials/culebrONT/config.yaml
/analysis/work/aswathy/projects/scott-linder/pacbio_assembly_pyoelii/trials/culebrONT/data/fastq
/analysis/work/aswathy/projects/scott-linder/pacbio_assembly_pyoelii/trials/culebrONT/data/refs/PlasmoDB-52_Pyoeliiyoelii17X_Genome.fasta
/analysis/work/aswathy/projects/scott-linder/pacbio_assembly_pyoelii/trials/culebrONT/culebrONT_OUTPUT

cant you try to write absolute path on your config.yaml like:

DATA:
    FASTQ: '/analysis/work/aswathy/projects/scott-linder/pacbio_assembly_pyoelii/trials/culebrONT/data/fastq/'
    FAST5: ''
    ILLUMINA: ''
    GENOME_SIZE: '23m'
    REF: '/analysis/work/aswathy/projects/scott-linder/pacbio_assembly_pyoelii/trials/culebrONT/data/refs/PlasmoDB-52_Pyoeliiyoelii17X_Genome.fasta'
    OUTPUT: '/analysis/work/aswathy/projects/scott-linder/pacbio_assembly_pyoelii/trials/culebrONT/culebrONT_OUTPUT/'

[aswathyseb]

Yes, that is a valid path.

Also I tried with absolute paths in my config file but still get the same error!

[sravel]

Ok I see the bug, on data_test you run on $HOME but here on /analysis/ try this: time culebrONT run_local -c config.yaml -t 15 --singularity-args "--bind /analysis/:/analysis/"

[aswathyseb]

Thank you. It looks like that was the problem. It is running...