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Jianwei-Zhang / DEGAP

Dynamic Elongation of a Genome Assembly Path
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SeqIO.index_db problem #1

Open lilinzhou opened 4 months ago

lilinzhou commented 4 months ago

Hi, when I run ctglinker, I got the error below, it seems there are some problem with the index_db. I used the latest biopython (1.8.0) can you help me to figure it out? BUILD RAWREADS DICT Traceback (most recent call last): File "/path/to/DEGAP/DEGAP.py", line 123, in readsdict=SeqIO.index_db(out+"/reads.idx",reads,"fasta") File "/path/to/Python-3.9.6/lib/python3.9/site-packages/Bio/SeqIO/init.py", line 999, in index_db return _SQLiteManySeqFilesDict( File "/path/to/Python-3.9.6/lib/python3.9/site-packages/Bio/File.py", line 323, in init self._load_index() File "/path/to/Python-3.9.6/lib/python3.9/site-packages/Bio/File.py", line 339, in _load_index (count,) = con.execute( TypeError: cannot unpack non-iterable NoneType object

HuangYicheng-Bio commented 1 month ago

Hi, when I run ctglinker, I got the error below, it seems there are some problem with the index_db. I used the latest biopython (1.8.0) can you help me to figure it out? BUILD RAWREADS DICT Traceback (most recent call last): File "/path/to/DEGAP/DEGAP.py", line 123, in readsdict=SeqIO.index_db(out+"/reads.idx",reads,"fasta") File "/path/to/Python-3.9.6/lib/python3.9/site-packages/Bio/SeqIO/init.py", line 999, in index_db return _SQLiteManySeqFilesDict( File "/path/to/Python-3.9.6/lib/python3.9/site-packages/Bio/File.py", line 323, in init self._load_index() File "/path/to/Python-3.9.6/lib/python3.9/site-packages/Bio/File.py", line 339, in _load_index (count,) = con.execute( TypeError: cannot unpack non-iterable NoneType object

Hi,

This issue arises from an incomplete indexing process. Possible reasons include: 1) Insufficient memory preventing the creation of reads.idx, and 2) If the process is run multiple times, the previous attempt may not have successfully created the reads.idx index, leading to errors when the second run skips the indexing step.

To resolve this, check your memory availability and delete the existing reads.idx index file from the output directory before re-running the process.

Best, Yicheng