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multi10x output path #31

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topherconley opened this Issue Dec 4, 2017 · 3 comments

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@topherconley

topherconley commented Dec 4, 2017

Hi,

Not sure where the .loom output file is located after running the following:

$velo multi10x -n 4 -l $log_folder -m $repmask $parentfolder $intervals

All I see in STDOUT is this:

2017-12-02 04:00:24,912 - DEBUG - Attempting to start 4 processes

Then I ran velocyto on each sample individually as a background process:

for sample_path in $parentfolder/*;
do
  echo $sample_path 
  sample=`basename $sample_path`
  $velo run10x -m $repmask $sample_path $intervals 1> logs_velocyto/${sample}.log 2> logs_velocyto/${sample}.err &
done

It seems to be running each sample in the background well enough right now:

2017-12-04 10:03:41,978 - DEBUG - Read first 100 million mapped reads
2017-12-04 10:05:21,292 - DEBUG - Marking up chromosome 17
2017-12-04 10:06:25,369 - DEBUG - Read first 110 million mapped reads
2017-12-04 10:08:30,929 - DEBUG - Marking up chromosome 18

Thus far I see a velocyto/ folder in the $sample_path,

Where is the output going to be? Perhaps make this more explicit in the documentation.

Any comments on the "multi10x" subcommand?

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topherconley Dec 4, 2017

The velocyto run10x command worked in just about 2.5 hours per sample as suggested and put the output in velocyto/sample_id.loom. This is reported in the log at the end of completion.

2017-12-04 11:46:06,268 - DEBUG - Generating output file $sample_path/velocyto/sample_01.loom

Glad it worked! It would be helpful to explain the velocyto subfolder output to the user in the docs.

topherconley commented Dec 4, 2017

The velocyto run10x command worked in just about 2.5 hours per sample as suggested and put the output in velocyto/sample_id.loom. This is reported in the log at the end of completion.

2017-12-04 11:46:06,268 - DEBUG - Generating output file $sample_path/velocyto/sample_01.loom

Glad it worked! It would be helpful to explain the velocyto subfolder output to the user in the docs.

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gioelelm Dec 4, 2017

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Thanks for the suggestions I will add some info to the docs about the velocyto subfolder. I was also thinking to maybe remove the command multi10x, as you probably figure out is just a shortcut that uses python subprocess to run several instances of of run10x, it is basically equivalent to what you are doing with your bash script.

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gioelelm commented Dec 4, 2017

Thanks for the suggestions I will add some info to the docs about the velocyto subfolder. I was also thinking to maybe remove the command multi10x, as you probably figure out is just a shortcut that uses python subprocess to run several instances of of run10x, it is basically equivalent to what you are doing with your bash script.

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topherconley Dec 8, 2017

No problem, happy that it is working as advertised.

topherconley commented Dec 8, 2017

No problem, happy that it is working as advertised.

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