list index out of range

[yl2005a]

Sorry to interrupt. It was my mistake:

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/lihaomei/.conda/envs/syri_env/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/lihaomei/.conda/envs/syri_env/lib/python3.9/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 "/home/lihaomei/.conda/envs/syri_env/bin/syri", line 6, in
main(sys.argv[1:])
File "/home/lihaomei/.conda/envs/syri_env/lib/python3.9/site-packages/syri/scripts/syri.py", line 326, in main
syri(args)
File "/home/lihaomei/.conda/envs/syri_env/lib/python3.9/site-packages/syri/scripts/syri.py", line 214, 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 "/home/lihaomei/.conda/envs/syri_env/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/lihaomei/.conda/envs/syri_env/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
IndexError: list index out of range

These are my orders, BAM files and fasta files are checked for errors.

syri -c minimap/filtered_file.bam -r /home/bioinfo/Fungi/02.Project/02.Pan-genome/Agaricus_bisporus/00.Data/GenomeData/A13_20.genome.fasta -q /home/lihaomei/08.Pan/04.syri_res/new4_2/minimap/new.4_3/fasta/H97.genome.fasta -F B

[2840976210]

。。。

[Surbhigrewal]

I'm getting the same error.

[yl2005a]

I found that if you align each of the chromosomes in the genome, you can do it.

…

---Original--- From: ***@***.***> Date: Thu, Jun 12, 2025 14:19 PM To: ***@***.***>; Cc: ***@***.******@***.***>; Subject: Re: [schneebergerlab/plotsr] list index out of range (Issue #98) Surbhigrewal left a comment (schneebergerlab/plotsr#98) I'm getting the same error. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Surbhigrewal]

You mean do one chromosome at a time?

[yl2005a]

no，Is to sequence each genome in a uniform way, all of which are aligned in the forward direction or the reverse direction.Unify them as positive or negative.You can try mummerplot  and correction of Chromosome Orientation by Reverse Complementarity,you can write a script.

…

---Original--- From: ***@***.***> Date: Thu, Jun 12, 2025 14:23 PM To: ***@***.***>; Cc: ***@***.******@***.***>; Subject: Re: [schneebergerlab/plotsr] list index out of range (Issue #98) Surbhigrewal left a comment (schneebergerlab/plotsr#98) You mean do one chromosome at a time? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>