error uploading files to local galaxy

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hi there I just installed a local galaxy server on my computer, and I loaded several fastq files with no problems while I have issues uploading 2 fastaq. I used these fastq in other analysis and they work just fine. this is the error I get:
Fatal error: Exit code 1 ()

Tool generated the following standard error:

Traceback (most recent call last):
File “/Users/azimmer/galaxy/tools/data_source/upload.py”, line 326, in
main()
File “/Users/azimmer/galaxy/tools/data_source/upload.py”, line 319, in main
metadata.append(add_file(dataset, registry, output_path))
File “/Users/azimmer/galaxy/tools/data_source/upload.py”, line 128, in add_file
convert_spaces_to_tabs=dataset.space_to_tab,
File “/Users/azimmer/galaxy/lib/galaxy/datatypes/upload_util.py”, line 54, in handle_upload
convert_spaces_to_tabs=convert_spaces_to_tabs,
File “/Users/azimmer/galaxy/lib/galaxy/datatypes/sniff.py”, line 759, in handle_uploaded_dataset_file_internal
if not is_binary and check_content and check_html(converted_path):
File “/Users/azimmer/galaxy/lib/galaxy/util/checkers.py”, line 28, in check_html
temp = open(file_path, mode=‘rb’)
IOError: [Errno 2] No such file or directory: u’/Users/azimmer/galaxy/database/tmp/f2db41e1fa331b3e-1570157510288-2428886529’

thanks for any help!

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2

Can you post the job_conf.xml file? what is the size of the files? if your files are bigger than 2Gb try to use ftp

3

@nibhelim How did you load the files into Galaxy? Does the file /Users/azimmer/galaxy/database/tmp/f2db41e1fa331b3e-1570157510288-2428886529 exist on the file system? Does it have the correct permissions?

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2 Likes
4

Hi, I am having similar issues. When I upload local files, they appear in my history, but they are empty and I’m getting “/bin/sh: /Users/viboud: No such file or directory”. The upload path is “/Users/viboud 1/galaxy/database/files/000/dataset_30.dat”, but that file doesn’t contain anything. Any advice?
Thank you!
Vincent

5

@viboud12 You have a space in your path… Change it to something like:
/Users/viboud_1/

1 Like
6

That worked thank you!!!

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