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schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
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high fraction of inverted alignments #163

Closed YuChrming closed 1 year ago

YuChrming commented 1 year ago

Good pipline to use easily! I met an error , how to solve it? syri -c out.sam -d out.best.delta -r HFTH1.all.chr.fa -q type03.fa -k -F S

Reading Coords - WARNING - Reference chromosome Chr07 has high fraction of inverted alignments with its homologous chromosome in the query genome (Chr07). Ensure that same chromosome-strands are being compared in the two genomes, as different strand can result in unexpected errors. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/ngsproject/qmyu/miniconda3/envs/syri/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/ngsproject/qmyu/miniconda3/envs/syri/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "syri/pyxFiles/synsearchFunctions.pyx", line 803, in syri.synsearchFunctions.syri IndexError: list index out of range """

Thanks a lot!

chhenyy commented 1 year ago

I met the same error, syri -c out.sam -r chr15_1.fasta -q chr15_2.fasta -k -F S

Reading Coords - WARNING - Reference chromosome chr15 has high fraction of inverted alignments with its homologous chromosome in the query genome (chr15). Ensure that same chromosome-strands are being compared in the two genomes, as different strand can result in unexpected errors. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/UserHome/user/miniconda3/envs/syri/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/UserHome/user/miniconda3/envs/syri/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "syri/pyxFiles/synsearchFunctions.pyx", line 803, in syri.synsearchFunctions.syri IndexError: list index out of range """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/UserHome/user/miniconda3/envs/syri/bin/syri", line 6, in main(sys.argv[1:]) File "/UserHome/user/miniconda3/envs/syri/lib/python3.8/site-packages/syri/scripts/syri.py ", line 319, in main syri(args) File "/UserHome/user/miniconda3/envs/syri/lib/python3.8/site-packages/syri/scripts/syri.py ", line 209, in syri startSyri(args, coords[["aStart", "aEnd", "bStart", "bEnd", "aLen", "bLen", "iden", "aDir", "bDir", "aChr", "bChr"]]) File "syri/pyxFiles/synsearchFunctions.pyx", line 505, in syri.synsearchFunctions.startSyri File "syri/pyxFiles/synsearchFunctions.pyx", line 506, in syri.synsearchFunctions.startSyri File "/UserHome/user/miniconda3/envs/syri/lib/python3.8/multiprocessing/pool.py", line 364 , in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/UserHome/user/miniconda3/envs/syri/lib/python3.8/multiprocessing/pool.py", line 771 , in get raise self._value IndexError: list index out of range

mnshgl0110 commented 1 year ago

Please ensure that same strands are being compared for the homologous chromosomes. Check https://github.com/schneebergerlab/syri/issues/48