I’m trying to get human plug’n play fasta reference blasted against itself from Trinity to use in STAR-fusion.
But I got the following error:
Dataset Error Report
An error occurred while running the tool upload1.Details
Execution resulted in the following messages:Fatal error: Exit code 1 ()
Tool generated the following standard error:Traceback (most recent call last):
File “/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py”, line 342, in
main()
File “/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py”, line 335, in main
metadata.append(add_file(dataset, registry, output_path))
File “/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py”, line 146, in add_file
convert_spaces_to_tabs=dataset.space_to_tab,
File “/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/upload_util.py”, line 54, in handle_upload
convert_spaces_to_tabs=convert_spaces_to_tabs,
File “/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/sniff.py”, line 730, in handle_uploaded_dataset_file_internal
auto_decompress=auto_decompress,
File “/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/sniff.py”, line 683, in handle_compressed_file
chunk = compressed_file.read(CHUNK_SIZE)
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/galaxy/lib/python3.6/gzip.py”, line 276, in read
return self._buffer.read(size)
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/galaxy/lib/python3.6/_compression.py”, line 68, in readinto
data = self.read(len(byte_view))
File “/cvmfs/main.galaxyproject.org/deps/_conda/envs/galaxy/lib/python3.6/gzip.py”, line 482, in read
raise EOFError("Compressed file ended before the "
EOFError: Compressed file ended before the end-of-stream marker was reached
The problem is that the file is 31gb and my personal upload is very slow, so direct upload from trinity would be easier!