Ingesting a gene annotation .bed file, Error: No such file or directory: '/tmp/geneAnnotationsExonUnionsMM39.bed.beddb'

[narzouni]

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:

  higlass-manage ingest geneAnnotationsExonUnionsMM39.bed --filetype bedfile --datatype bedlike  --assembly mm39 

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'

[pkerpedjiev]

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

[narzouni]

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.

[narzouni]

[narzouni]

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.