yangli557 / annosine Goto Github PK

Hi there
I would like to thank all the AnnoSINE developers !
I'm trying to run this software on Ubuntu Linux, and it seems that the code as optimized for MacOSX.
trf and irf binaries should be correctly explicitly in the py scripts.
However, the A. thaliana test example is taking more than 2 hours to run on a 40CPU server, and not 7 minutes as stated on the README.
Other genomes, ranging 500mb is taking more than 2 day to run (not finished yet). This is normal ?

Hi,

Can we use AnnoSINE to annotate animal genomes? Why or why not?

Best,
Kun

Hi thank you for developing this tool.

there is problem in installing prerequest tools mainly for repeatmasker

So, Could you provide a docker image, or singularity

with regards

Hi,

I am trying the install the prerequisites, but the inverted repeat finder (IRF 3.05 source is not available. Maybe it's just a problem from my site but I would appreciate it to know where else I can get it from. Thanks.

Rom

@yangli557 I don't see how you can give the number of CPUs to run AnnoSINE. The process is pretty slow.

Hi there!
I'm trying to run AnnoSINE, but always I have same error, as above. I tried to use other sequences for testing.
The running command is in the /bin folder. Can anyone shed a light on it? Thankss

Error:

======================== Step 1 has been done ========================

================ Step 2: TSD identification has begun ================
/home/eniac/jordana/AnnoSINE/bin/TSD_Searcher.js:133
const FNA_PATTERN = new RegExp(FNA_HEAD_PATTERN + FNA_SEQUENCE_PATTERN, "g");
^

SyntaxError: Invalid regular expression: /(?>[^]*
)(?[atcgATCG
]+)/: Invalid group
at new RegExp ()
at Object. (/home/eniac/jordana/AnnoSINE/bin/TSD_Searcher.js:133:21)
at Module._compile (module.js:652:30)
at Object.Module._extensions..js (module.js:663:10)
at Module.load (module.js:565:32)
at tryModuleLoad (module.js:505:12)
at Function.Module._load (module.js:497:3)
at Function.Module.runMain (module.js:693:10)
at startup (bootstrap_node.js:188:16)
at bootstrap_node.js:609:3
Traceback (most recent call last):
File "AnnoSINE.py", line 1174, in
main_function()
File "AnnoSINE.py", line 1125, in main_function
process_tsd_output(input_genome_assembly_path, output_genome_assembly_path)
File "AnnoSINE.py", line 301, in process_tsd_output
with open(filename) as f2:
FileNotFoundError: [Errno 2] No such file or directory: '../Testing/output/Step2_tsd.txt'

Dear Yang,

Great work! Congratulations!

I am so excited to learn that finally there is a good tool for de novo SINE annotation! Before attempting to try to use it on my side, I notice that the repo does not have a software license. Without a license, it will be difficult to make distributions such as conda. Can you please add one? For open source licensing, usually, people use MIT or the GNU General Public License. Please let me know if you need help.

Best,
Shujun

Dear developer:
I met such error below:
AnnoSINE_v2 -t 10 -a 2 --num_alignments 50000 -rpm 0 --copy_number 3 --shift 100 -auto 1 3 genome.fa ./
Example: AnnoSINE_v2 3 ../Input_Files/test.fasta ../Output_Files
Please input the path of genomic sequence

*************************** AnnoSINE START! ****************************

====== Step 1: HMMER prediction and structure search has begun =======
Step1_process_hmm not finished! Will regenerate the result!

Step 1 mode-3::hmm_predict uses 36.732131242752075 s
process_hmm_output_3:read_genome_assembly uses 0.002218484878540039
Processing the hmm prediction ...
process_hmm_output_3:process_hmm_output_2_r1 uses 0.03598666191101074
Processing the hmm prediction ...
process_hmm_output_3:process_hmm_output_2_r2 uses 0.01045846939086914
Processing the hmm prediction ...
process_hmm_output_3:process_hmm_output_2_r3 uses 0.010227441787719727
process_hmm_output_3:merge_same_hmm_output uses 6.103515625e-05
process_hmm_output_3:for_loop uses 2.002716064453125e-05
Step 1 mode-3::process_hmm_output_3 uses 0.061069488525390625 s
Step1_sine_part not finished! Will regenerate the result!
Step 1 mode-3::sine_finder uses 2.8167171478271484 s
Step 1 mode-3::process_sine_finder uses 0.002566814422607422 s
Step1_merge_part not finished! Will regenerate the result!
Step 1::merge_tsd_input uses 0.0011138916015625 s
Step 1 totally uses 39.61408591270447 s

======================== Step 1 has been done ========================

================ Step 2: TSD identification has begun ================
Step2_search_tsd not finished! Will regenerate the result!
Successfully split the file into 1 chunks, with a maximum of 1000 lines per chunk.
/Share/user/liyilou/miniconda3/envs/EDTA2/lib/python3.10/site-packages/AnnoSINE/TSD_Searcher_multi.js:138
const FNA_PATTERN = new RegExp(FNA_HEAD_PATTERN + FNA_SEQUENCE_PATTERN, "g");
^

SyntaxError: Invalid regular expression: /(?>[^]*
)(?[atcgATCGNnXx
]+)/: Invalid group
at RegExp (native)
at Object. (/Share/user/liyilou/miniconda3/envs/EDTA2/lib/python3.10/site-packages/AnnoSINE/TSD_Searcher_multi.js:138:21)
at Module._compile (module.js:577:32)
at Object.Module._extensions..js (module.js:586:10)
at Module.load (module.js:494:32)
at tryModuleLoad (module.js:453:12)
at Function.Module._load (module.js:445:3)
at Module.runMain (module.js:611:10)
at run (bootstrap_node.js:387:7)
at startup (bootstrap_node.js:153:9)
Traceback (most recent call last):
File "/Share/user/liyilou/miniconda3/envs/EDTA2/bin/AnnoSINE_v2", line 10, in
sys.exit(main())
File "/Share/user/liyilou/miniconda3/envs/EDTA2/lib/python3.10/site-packages/AnnoSINE/AnnoSINE_v2.py", line 1707, in main
search_tsd(output_genome_assembly_path, script_dir,cpus)
File "/Share/user/liyilou/miniconda3/envs/EDTA2/lib/python3.10/site-packages/AnnoSINE/AnnoSINE_v2.py", line 544, in search_tsd
f=open(s,'r')
FileNotFoundError: [Errno 2] No such file or directory: './/TSD_output_chunk_1.fa'

Do you have any idea what's wrong with this?