Open narzouni opened 1 month ago
Is there any other output before that?
higlass-manage
should have tried to aggregate your bedfile and then ingest it:
https://github.com/higlass/higlass-manage/blob/master/higlass_manage/ingest.py#L154
I looked at the higlass-manage code before, and I realized it will aggregate the bed file to create the .beddb, but it was still giving the above errors. I think I was able to find the issue. It was in the chromsizes file. however, I was expecting to see the gene names displayed. Is there any way to do that? when I created the file geneAnnotationsExonUnionsMM39.bed
, I followed the link in my initial message. However, if I hover over the notation, I can see the names displayed. I was just hoping that it will display the name without hovering because I saw that in some higlass
docs. Thank you so much.
I was expecting to see the names of the genes, but I get the above attached image. It is good enough if there is no solution because if I hover over it, I can see the information.
Hello,
I have a question about an issue using
higlass-manage
. I hope I receive some feedback.I am trying to ingest a gene annotation .bed file, so I can see the gene labels on higlass visualization of .mcool files.
I created the file
geneAnnotationsExonUnionsMM39.bed
file based on the following link:https://docs.higlass.io/data_preparation.html#gene-annotation-tracks
I am trying to ingest the file using the following command:
I also tried using
--datatype gene-annotation
, but both gave me the error below.It gives the following error:
command: python higlass-server/manage.py ingest_tileset --filename /tmp/geneAnnotationsMM39.bed.beddb --filetype beddb --datatype bedlike --project-name "PenaLabHiCData" --coordSystem mm39 --uid A_hYkLnSTDqVIRkl6ELaiQ ERROR: Traceback (most recent call last): File "higlass-server/manage.py", line 22, in
execute_from_command_line(sys.argv)
File "/usr/local/lib/python3.8/dist-packages/django/core/management/init.py", line 381, in execute_from_command_line
utility.execute()
File "/usr/local/lib/python3.8/dist-packages/django/core/management/init.py", line 375, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/usr/local/lib/python3.8/dist-packages/django/core/management/base.py", line 323, in run_from_argv
self.execute(*args, *cmd_options)
File "/usr/local/lib/python3.8/dist-packages/django/core/management/base.py", line 364, in execute
output = self.handle(args, options)
File "/home/higlass/projects/higlass-server/tilesets/management/commands/ingest_tileset.py", line 236, in handle
ingest(options)
File "/home/higlass/projects/higlass-server/tilesets/management/commands/ingest_tileset.py", line 80, in ingest
django_file = File(open(filename,'rb'))
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/geneAnnotationsMM39.bed.beddb'