Dominik Lindner

👍 Thanks Will, seems to work now. I'll carry on converting idr0004 then and upload to biostudies.

Converted and uploaded to Biostudies.

On pilot-zarr2-dev: Converting one plate takes ~30min, zipping ~50min (without compression 7min!). Converted plate size 36Gb, zipped 28Gb. 7zip (p7zip): 5min (also 28Gb), (without compression 4min) There are 538 plates...

Created batch directories for each 10 plates under /data/ngff/idr0013 . Trying to do 10 conversions and 10 zip/uploads/delete a time, due to the disk space limitation.

For conversion: ``` cd /data/ngff/idr0013/batch_XX for i in `cat ../batch_XX.txt`; do ~/bioformats2raw/bin/bioformats2raw --memo-directory ../../memo /uod/idr/metadata/idr0013-neumann-mitocheck/screens/$i ${i%.*}.ome.zarr; done # Note: The input file batch_XX.txt is one directory up in /data/ngff/idr0013 !...

Failing plate: ``` (base) [dlindner@pilot-zarr2-dev batch_3]$ ~/bioformats2raw/bin/bioformats2raw --memo-directory ../../memo /uod/idr/metadata/idr0013-neumann-mitocheck/screens/LT0012_29--ex2005_06_10--sp2005_04_08--tt16--c3.screen LT0012_29--ex2005_06_10--sp2005_04_08--tt16--c3.ome.zarr OpenJDK 64-Bit Server VM warning: You have loaded library /tmp/opencv_openpnp3633973597553018286/nu/pattern/opencv/linux/x86_64/libopencv_java342.so which might have disabled stack guard. The VM will...

Wrapped it all into one script: ``` #!/bin/bash # Usage: ./run.sh screens.txt log.txt # Disable all output exec 2>&1 1>/dev/null for i in `cat $1`; do date >> $2 echo...

This is currently doing 3 conversions in a bit more than an hour. So should all be done in ~8 days.

Finished. Only `LT0012_29--ex2005_06_10--sp2005_04_08--tt16--c3.screen` failed conversion (see above).

Really finished now, exported the LT0012_29 plate with omero cli zarr. (LT0012_29.ome.zarr.zip)