I’m running a local galaxy instance on my desktop and I was trying to use the data managers to install the hg38 genome reference. I tried rsync as well which didn’t work. It was installed but wouldn’t open when I went to the data managers tab and clicked on it. So instead I’m trying the fasta fetcher, picard, etc way and when I run FASTA fetcher I’ve been getting this error.
Fatal error: Exit code 1 ()
Traceback (most recent call last):
File "/home/jgoodman/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/4d3eff1bc421/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 497, in <module>
main()
File "/home/jgoodman/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/4d3eff1bc421/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 478, in main
tmp_dir=tmp_dir)
File "/home/jgoodman/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/4d3eff1bc421/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 300, in download_from_ucsc
url = _get_ucsc_download_address(params, dbkey)
File "/home/jgoodman/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/4d3eff1bc421/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 260, in _get_ucsc_download_address
path_contents = _get_files_in_ftp_path(ftp, ucsc_path)
File "/home/jgoodman/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/4d3eff1bc421/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py", line 65, in _get_files_in_ftp_path
ftp.retrlines('MLSD %s' % (path), path_contents.append)
File "/home/jgoodman/galaxy/database/dependencies/_conda/envs/__python@3.7/lib/python3.7/ftplib.py", line 475, in retrlines
with self.transfercmd(cmd) as conn, \
File "/home/jgoodman/galaxy/database/dependencies/_conda/envs/__python@3.7/lib/python3.7/ftplib.py", line 406, in transfercmd
return self.ntransfercmd(cmd, rest)[0]
File "/home/jgoodman/galaxy/database/dependencies/_conda/envs/__python@3.7/lib/python3.7/ftplib.py", line 368, in ntransfercmd
source_address=self.source_address)
File "/home/jgoodman/galaxy/database/dependencies/_conda/envs/__python@3.7/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/home/jgoodman/galaxy/database/dependencies/_conda/envs/__python@3.7/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
BlockingIOError: [Errno 11] Resource temporarily unavailable
Despite trying multiple different days at different times of day, I still run into the resource temporarily unavailable error. Any help would be greatly appreciated!
not sure if that’s a problem with your Galaxy instance since I cannot currently get a directory listing of e.g. goldenPath/hg38/bigZips from the command line or with filezilla either.
Status: Resolving address of hgdownload.cse.ucsc.edu
Status: Connecting to 128.114.119.163:21...
Status: Connection established, waiting for welcome message...
Status: Insecure server, it does not support FTP over TLS.
Status: Logged in
Status: Retrieving directory listing of "/goldenPath/hg38/bigZips"...
Command: CWD /goldenPath/hg38/bigZips
Response: 250 CWD command successful
Command: PWD
Response: 257 "/apache/htdocs/goldenPath/hg38/bigZips" is the current directory
Command: TYPE I
Response: 200 Type set to I
Command: PASV
Response: 227 Entering Passive Mode (128,114,119,163,164,245).
Command: MLSD
Error: Connection timed out after 120 seconds of inactivity
Error: Failed to retrieve directory listing
Is there a known issue with UCSC’s ftp server atm?
That job ran without issues but then I tried running the SAM index builder afterwards and ran into an error, which I why I was trying to get the UCSC to work thinking it could get around this. The error SAM indexer shows is:
Error building index:
Traceback (most recent call last):
File "/home/jgoodman/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py", line 87, in <module>
if __name__ == "__main__": main()
File "/home/jgoodman/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py", line 82, in main
build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
File "/home/jgoodman/galaxy/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/2a1ac1abc3f7/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.py", line 48, in build_sam_index
sys.stderr.write( chunk )
TypeError: write() argument must be str, not bytes
I should note that TwoBit, Picard index, and HISAT2 indexers work without issue.
now that is a very(!) outdated version of the data manager from Aug 2015. Not sure why you have this one installed, but it’s likely still expecting Python2, not Python3.
Just go back to the Admin interface and install the latest version of the data manager and things should work.
