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slowkow / picardmetrics

:vertical_traffic_light: Run Picard on BAM files and collate 90 metrics into one file.
https://slowkow.github.io/picardmetrics
MIT License
39 stars 7 forks source link

ERROR: Please install the 'stats' program #10

Open schmittel opened 3 years ago

schmittel commented 3 years ago

I'm having a similar issue to https://github.com/slowkow/picardmetrics/issues/6 . When I run picardmetrics I get:

2020-11-18 08:16:00 picardmetrics config: '/cd16/software/picardmetrics/picardmetrics.conf' ERROR: Please install the 'stats' program https://github.com/arq5x/filo

The output of which stats is:

/cd16/software/bin/bin/stats

I've tried copying the stats bin to /usr/local/bin as well and echo $PATH does include stats.

This is the command I'm running:

for bam in cd16/hisat2/*.bam;
do \
/cd16/software/picardmetrics/picardmetrics run -f /cd16/software/picardmetrics/picardmetrics.conf -k -r -o /cd16/picard_metrics $bam; \
done

Many thanks

schmittel commented 3 years ago

Solved it. Have to run picardmetrics outside of a conda environment.