Batch processing Level 2 OLCI scenes

I am trying to batch processing a subset xml graph on L2 S3 images. My subset xml graph and processDataset.bash are attached. I am doing this call:

./processDataset.bash subset_6.xml "/media/silsbelab/S31/S3_L2/S3A_20160216_20190724" "/media/silsbelab/S31/S3_L2/Subset_S3_L2/" subset_S3_L2

I keep getting this error “[NodeId: ReadOp@sourceProduct] Specified ‘file’ [/media/silsbelab/S31/S3_L2/S3A_20160216_20190724/S3A_OL_2_WFR____20160426T144453_20160426T144653_20171030T174540_0119_003_253______MR1_R_NT_002.SEN3:] does not exist.”

There is a semicolon after the file which is strange and I can’t figure out how to delete it. Can someone please let me know if there is something wrong in either my xml graph or bash script?

processDataset.bash (1.5 KB) subset_6.xml (783 Bytes)

I am still having issues with this, if anyone is able to help troubleshoot, I’d greatly appreciate it.

Have you tried first to run from command line one scene? The call should be something like:

gpt_directory xml_directory -t target_scene_directory source_scene_directory

For running a shell you only need to write it and call it wit: sh$

I just tried running one scene from command line using this call:

/home/silsbelab/snap/bin/gpt /media/silsbelab/S31/S3_L2/subset_6.xml -t /media/silsbelab/S31/S3_L2/Subset_S3_L2/ /media/silsbelab/S31/S3_L2/S3A_20160216_20190724/S3A_OL_2_WFR____20160426T144453_20160426T144653_20171030T174540_0119_003_253______MR1_R_NT_002.SEN3

It ran, but made a new folder called which has .hdr and .img files within it. I would like just 1 .nc file that contains everything.

I think you missed to add the name of the output file and the extension in your command after /media/silsbelab/S31/S3_L2/Subset_S3_L2/

great, that worked! Can you help me with the batch processing? I’m confused by how to call it- do I save the call as a .sh file?