haydenm
commented
2 years ago I see this was closed before I could respond, but I just wanted to comment that I am unable to reproduce the error. Because it had to do with downloading information from NCBI GenBank, I'm hoping the error was transient and resolved itself. If that's not the case, I'm happy to help figure out a solution.
FyisFe
2022-02-23 17:02:05,101 - catch.utils.ncbi_neighbors [INFO] Creating a FASTA file for taxid 64320 2022-02-23 17:02:05,102 - catch.utils.ncbi_neighbors [INFO] Constructing a list of neighbors for taxid 64320 2022-02-23 17:03:56,248 - catch.utils.ncbi_neighbors [INFO] There are 1596 neighbors, 799 of which have unique accessions Traceback (most recent call last): File "/Users/yfeng/opt/anaconda3/lib/python3.8/http/client.py", line 555, in _get_chunk_left chunk_left = self._read_next_chunk_size() File "/Users/yfeng/opt/anaconda3/lib/python3.8/http/client.py", line 522, in _read_next_chunk_size return int(line, 16) ValueError: invalid literal for int() with base 16: b''
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/Users/yfeng/opt/anaconda3/lib/python3.8/http/client.py", line 572, in _readall_chunked chunk_left = self._get_chunk_left() File "/Users/yfeng/opt/anaconda3/lib/python3.8/http/client.py", line 557, in _get_chunk_left raise IncompleteRead(b'') http.client.IncompleteRead: IncompleteRead(0 bytes read)
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/Users/yfeng/opt/anaconda3/bin/design.py", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/Users/yfeng/Desktop/catch/bin/design.py", line 856, in
main(args)
File "/Users/yfeng/Desktop/catch/bin/design.py", line 66, in main
ds_fasta_tf = ncbi_neighbors.construct_fasta_for_taxid(taxid,
File "/Users/yfeng/Desktop/catch/catch/utils/ncbi_neighbors.py", line 465, in construct_fasta_for_taxid
seqs_tf = fetch_fastas(acc_to_fetch)
File "/Users/yfeng/Desktop/catch/catch/utils/ncbi_neighbors.py", line 207, in fetch_fastas
raw_data = r.read()
File "/Users/yfeng/opt/anaconda3/lib/python3.8/http/client.py", line 465, in read
return self._readall_chunked()
File "/Users/yfeng/opt/anaconda3/lib/python3.8/http/client.py", line 579, in _readall_chunked
raise IncompleteRead(b''.join(value))
http.client.IncompleteRead: IncompleteRead(536576 bytes read)