plant720 / easy353 Goto Github PK

Hi,
I meet error during ues easy353, as following. I do not know why, can you provide me with solution? Thank you so much！

Process Process-3:
Traceback (most recent call last):
File "/data/software/anaconda3/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/data/software/anaconda3/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/data/hbs/software/Easy353/Easy353Lib/filter.py", line 217, in reads_bin_filter
for file_index in filter_read_for_ref(ref_kmer_dict, k_size, s_size, read_seqs_lst, len(ref_path_lst),
File "/data/hbs/software/Easy353/Easy353Lib/filter.py", line 170, in filter_read_for_ref
bin_read_seq, read_len = dnaseq2int(read_seqs_lst[0])
File "/data/hbs/software/Easy353/Easy353Lib/filter.py", line 76, in dnaseq2int
return int(dna_seq, 4), len(dna_seq)
ValueError: invalid literal for int() with base 4: '13000021000011020000300030111001030321303112100030030030100011100001111101300300000103010111001110030031311000310000003011100300011001110113020201110FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF:FF:'
Process Process-6:
Traceback (most recent call last):
File "/data/software/anaconda3/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/data/software/anaconda3/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/data/hbs/software/Easy353/Easy353Lib/filter.py", line 217, in reads_bin_filter
for file_index in filter_read_for_ref(ref_kmer_dict, k_size, s_size, read_seqs_lst, len(ref_path_lst),
File "/data/hbs/software/Easy353/Easy353Lib/filter.py", line 170, in filter_read_for_ref
bin_read_seq, read_len = dnaseq2int(read_seqs_lst[0])
File "/data/hbs/software/Easy353/Easy353Lib/filter.py", line 76, in dnaseq2int
return int(dna_seq, 4), len(dna_seq)
ValueError: invalid literal for int() with base 4: '13000021000011020000300030111001030321303112100030030030100011100001111101300300000103010111001110030031311000310000003011100300011001110113020201110FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF:FF:'
……………………

Hi,
How to use unpaired reads to run easy353 in Linux system? I seem to not find the parameter setting.

Hi
I have been experiencing this error while using the easySFS and I have no idea how to fix it.
Thanks, Looking forward to your reply.

easy353.py -1 HKXS02_R1.fq.gz -2 HKXS02_R2.fq.gz -o out_try -r ~/software/353_ref_Gesneriaceae/353gene/

usage: easy353.py [options]
easy353.py: error: unrecognized arguments: -1 HKXS02_R1.fq.gz -2 HKXS02_R2.fq.gz -o out_try -r /public/home/lifengrong/software/353_ref_Gesneriaceae/353gene/

hello,
I used fdog (https://github.com/BIONF/fDOG) to construct a reference sequence (amino acid sequence) based on which I would like to use easy353 to identify homologous genes in other species sequencing data. Does easy353 not recognize the reference sequence of the amino acid sequence? What should I do?

您好：
我在运行软件的时候，遇到了以下问题，麻烦向您请教一下如何解决，谢谢！

command line:
easy353.py -1 E100071774_L01_UDB4_NT01_R1.fq.gz -2 E100071774_L01_UDB4_NT01_R2.fq.gz -r ~/software/Easy353-master/353_ref_Gesneriaceae/353gene/ -o E100071774_L01_UDB4_NT01_gzout_353 -k1 31 -k2 41 -t1 32 -t2 32
error message：
usage: easy353.py [options]
easy353.py: error: unrecognized arguments: -k1 31 -k2 41 -t1 32 -t2 32

command line:
easy353.py -1 E100071770_L01_UDB103_DMDT01_R1.fq.gz -2 E100071770_L01_UDB103_DMDT01_R2.fq.gz -r ~/software/Easy353-master/353_ref_Gesneriaceae/353gene/ -o E100071770_L01_UDB103_DMDT01_gzout_353 -t1 32 -t2 32
error message：
usage: easy353.py [options]
easy353.py: error: unrecognized arguments: -t1 32 -t2 32

Thank you very much for your excellent work!
I am trying to assemble reads from Angiosperms353 sequences.
I am facing the following issue: After using build_database.py following the pattern in the docs, I run easy353.py. However, while it hashes the same (number of) sequences as from the GUI, it then proceeds to align only a very small number of "genes". Upon checking the assembly output, I discover that Easy353 attempted to assemble against the individuals from the reference library rather than the 353 genes, leading to nonsense output.

Using the GUI, I enter the family name as the taxon for fetching the reference genes, and then recover essentially all gene regions, which is great.
So the issue only seems to affect the command line version.
However, I have many individuals, so I do need to use the command line version to allow for scripting.
I have tested this under both Ubuntu Linux and MS Windows, with the same outcome.
Any help would be appreciated!

In Easys353 Windows GUI, if the filtering threads is setting to more than one, the process will stuck at “Filter reads from fq_files based on hash table with xx thread”. I also received similar feedback from others. Hope it can be solved.
Platform: 13th Intel core processor with Windows 10 22H2