Comments (6)
mnshgl0110
commented on August 21, 2024
Hi. SyRI requires the CIGAR strings to have '=' for match and 'X' for mismatch. While running minimap2, please use --eqx parameter (https://lh3.github.io/minimap2/minimap2.html). That should generate the SAM file in the required format.
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jhawkey
commented on August 21, 2024
Thanks! I clearly missed this when looking at the working example page in the documentation.
I can now get syri to run (using the same command as above), but it's now apparently having issues with chromosome IDs (see error below).
I'm also attaching the log file in case that is helpful.
syri.log
./syri/syri/bin/syri -c MINF_9D_vs_MSB1_6J_minimap.sam -r MINF_9D.fasta -q MSB1_6J.fasta -F S --log DEBUG
syri - WARNING - starting
Reading Coords - WARNING - Chromosomes IDs do not match.
Reading Coords - WARNING - Matching them automatically. For each reference genome, most similar query genome will be selected. Check mapids.txt for mapping used.
('invOut.txt', ' is empty. Skipping analysing it.')
('TLOut.txt', ' is empty. Skipping analysing it.')
ctxOut.txt is empty. Skipping analysing it.
('inv', 'Out.txt is empty. Skipping analysing it.')
('TL', 'Out.txt is empty. Skipping analysing it.')
('dup', 'Out.txt is empty. Skipping analysing it.')
('invDup', 'Out.txt is empty. Skipping analysing it.')
ctxOut.txt is empty. Skipping analysing it.
Reading Coords - WARNING - Chromosomes IDs do not match.
Reading Coords - WARNING - Matching them automatically. For each reference genome, most similar query genome will be selected. Check mapids.txt for mapping used.
('invOut.txt', ' is empty. Skipping analysing it.')
('TLOut.txt', ' is empty. Skipping analysing it.')
ctxOut.txt is empty. Skipping analysing it.
Traceback (most recent call last):
File "/Users/jane/miniconda3/envs/syri/lib/python3.5/site-packages/pandas/core/indexes/base.py", line 3078, in get_loc
return self._engine.get_loc(key)
File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'id'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./syri/syri/bin/syri", line 179, in <module>
getTSV(args.dir, args.prefix, args.ref.name)
File "syri/pyxFiles/writeout.pyx", line 171, in syri.writeout.getTSV
File "/Users/jane/miniconda3/envs/syri/lib/python3.5/site-packages/pandas/core/frame.py", line 2688, in __getitem__
return self._getitem_column(key)
File "/Users/jane/miniconda3/envs/syri/lib/python3.5/site-packages/pandas/core/frame.py", line 2695, in _getitem_column
return self._get_item_cache(key)
File "/Users/jane/miniconda3/envs/syri/lib/python3.5/site-packages/pandas/core/generic.py", line 2489, in _get_item_cache
values = self._data.get(item)
File "/Users/jane/miniconda3/envs/syri/lib/python3.5/site-packages/pandas/core/internals.py", line 4115, in get
loc = self.items.get_loc(item)
File "/Users/jane/miniconda3/envs/syri/lib/python3.5/site-packages/pandas/core/indexes/base.py", line 3080, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 140, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 162, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1492, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1500, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'id'
Thanks!
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mnshgl0110
commented on August 21, 2024
Can you please also share the corrected SAM file? Thanks
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jhawkey
commented on August 21, 2024
MINF_9D_vs_MSB1_6J_minimap.sam.txt
Yes, here it is!
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mnshgl0110
commented on August 21, 2024
Hi Jane, thanks for sharing the file. There were some uncaught exceptions which were causing issues with your data ('genomes' without structural variations were not expected). I have modified the script and it should finish properly without complaining about it. Please download and re-install SyRI, and rerun the analysis.
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jhawkey
commented on August 21, 2024
Thank you!
…On 21 Dec 2019, 12:03 AM +1100, Manish Goel ***@***.***>, wrote:
Hi Jane, thanks for sharing the file. There were some uncaught exceptions which were causing issues with your data ('genomes' without structural variations were not excepted). I have modified the script and it should finish properly without complaining about it. Please download and re-install SyRI, and rerun the analysis.
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Related Issues (20)
- The question with "Unequal number of chromosomes in the genomes" error HOT 1
- Issue of choice of aligner for whole genome alignment of two set of genomes HOT 2
- SAM reader - ERROR - Incorrect CIGAR string found. CIGAR string can only have I/D/H/S/X/=. CIGAR STRING: CM028859.1 HOT 2
- Cython package not detected HOT 3
- Erro in reading BAM file. reference_id -1 out of range HOT 1
- Synteny differs between same set of assemblies HOT 5
- Genome specific sequences HOT 3
- Chromosomes IDs do not match HOT 2
- IndexError: list index out of range (but no error when swapping the reference and query) HOT 7
- generating table output error HOT 2
- Error when using .SAM file HOT 18
- Incorrect CIGAR string found. HOT 6
- unequal chromosomes HOT 3
- empty output of chroder HOT 6
- AttributeError with syri HOT 1
- IndexError: list index out of range HOT 5
- missing parameter HOT 1
- REF and ALT start positions do not match HOT 1
- ERROR - syri:116 - Unequal number of chromosomes in the genomes. HOT 6
- Support of bgzip fasta HOT 1
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