conda running code

[desmodus1984]

conda running code

[bistace]

Hello,

on conda, you can just invoke hapog.py as it will be in your PATH.

[desmodus1984]

Hello,

on conda, you can just invoke hapog.py as it will be in your PATH.

Hi I ran the following command:
hapog --genome /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta # Fasta file of the genome to polish
-b ../MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam -o myse -t 48

and I got the following message:
usage: hapog [-h] --genome INPUT_GENOME [--pe1 PE1] [--pe2 PE2]
[--single LONG_READS] [-b BAM_FILE] [-u] [--output OUTPUT_DIR]
[--threads THREADS] [--bin HAPOG_BIN]
hapog: error: unrecognized arguments:
/var/spool/slurmd/job5287196/slurm_script: line 12: -b: command not found

What am I doing wrong?

[bistace]

Hi,

if you copied and pasted the entire command line you ran in your previous comment, you have forgotten to include line breaks. Basically, bash will understand that you tried to run the following two commands:

First one:

hapog --genome /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta # Fasta file of the genome to polish

Second one:

-b ../MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam -o myse -t 48

As you can see, these are probably not the ones you intended to run.

Instead, I recommend that you run (assuming the input files are correct):

hapog --genome /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta  -b ../MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam -o myse -t 48

You can also use this multi-lines version (notice the new line breaks):

hapog --genome  /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta \
    -b ../MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam \
    -o myse \
    -t 48

[desmodus1984]

Hi,

if you copied and pasted the entire command line you ran in your previous comment, you have forgotten to include line breaks. Basically, bash will understand that you tried to run the following two commands:

First one:

hapog --genome /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta # Fasta file of the genome to polish

Second one:

-b ../MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam -o myse -t 48

As you can see, these are probably not the ones you intended to run.

Instead, I recommend that you run (assuming the input files are correct):

hapog --genome /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta  -b ../MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam -o myse -t 48

You can also use this multi-lines version (notice the new line breaks):

hapog --genome  /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta \
    -b ../MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam \
    -o myse \
    -t 48

Hi,

I just did that; I used the following code:

hapog --genome /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta \
        -b /fs/scratch/PHS0338/appz/MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam \
        -o myse \
        -t 48

I even checked if hapo-g was installed in conda and it is, and I got the following error:
/var/spool/slurmd/job5303212/slurm_script: line 11: hapog: command not found

I am very confused because, when it was close to work the error was:
usage: hapog [-h] --genome INPUT_GENOME [--pe1 PE1] [--pe2 PE2]
[--single LONG_READS] [-b BAM_FILE] [-u] [--output OUTPUT_DIR]
[--threads THREADS] [--bin HAPOG_BIN]
hapog: error: unrecognized arguments:
/var/spool/slurmd/job5287196/slurm_script: line 12: -b: command not found

and now I am using hapog and it is not running.

[bistace]

Hello,

this is weird. I just checked on my system with a fresh installation and everything seems to work.

Here is what I think you should do:

1. Create a fresh conda env for hapog (make sure you are in the base env while running this):

conda env remove --name hapog (replace hapog by the name of your conda env)
conda create -n hapog
conda activate hapog
conda install -c lbgb_cea hapog

2. Execute hapog by invoking hapog.pywhich is the wrapper script (make sure that you are in the hapog conda env that you just created and installed hapog into):

hapog.py --genome /users/PHS0338/jpac1984/data/SuperExt.scaff.fasta \
        -b /fs/scratch/PHS0338/appz/MaSuRCA-4.0.5/TGI_myse/SuperExt.scaff.fasta.alignSorted.bam \
        -o myse \
        -t 48