caozhichongchong / i-vip Goto Github PK

A trial version of I-VIPv1.0 for python ≥ 3.0 (I-VIPv1.0_py3) is released.
Please contact [email protected] if there's any problem running this version.
For python < 3.0, please use the original version of I-VIPv1.0 (https://github.com/caozhichongchong/I-VIP/releases).
I-VIPv1.0_py3.zip

Hi There,
This is a great tool for identifying integrons, however I have been trying to get it to work and keep having some problems.

I end up with empty files in the Integron folder and also, the location that the script looks for the BLASTP results comes back empty.

Here is the integron files, you can see they are all empty
total 8.0K
drwxrwxr-x 7 harbj019 harbj019 4.0K Jan 31 17:39 ClassI
drwxrwxr-x 7 harbj019 harbj019 4.0K Jan 31 17:39 Other
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Genbank_annotation.ClassI.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Genbank_annotation.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integrase_seqs.ClassI.fasta
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integrase_seqs.fasta
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integron_seqs.ClassI.fasta
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integron_seqs.fasta
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integron_structure.ClassI.annotated.formated.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integron_structure.ClassI.annotated.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integron_structure.ClassI.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integron_structure.annotated.formated.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integron_structure.annotated.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.Integron_structure.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.ClassI.fasta
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.ClassI.fasta.ARG.blast.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.ClassI.fasta.ARG.blast.txt.filter.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.ClassI.fasta.MRG.blast.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.ClassI.fasta.MRG.blast.txt.filter.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.fasta
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.fasta.ARG.blast.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.fasta.ARG.blast.txt.filter.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.fasta.MRG.blast.txt
-rw-rw-r-- 1 harbj019 harbj019 0 Jan 31 17:39 all.ORFs.fasta.MRG.blast.txt.filter.txt

here are the results when the files cant be found:

python /home/harbj019/softwarebins/I-VIP.v1.2.py3/scripts/Integron_extraction.py -i /home/harbj019/softwarebins/I-VIP.v1.2.py3/metas --g None --r I-VIP_result --f .fa --o .faa

cat: 'I-VIP_result/Integron/Other/Genbank_annotation/': No such file or directory
cat: 'I-VIP_result/Integron/Other/Integrase_seqs/': No such file or directory
cat: 'I-VIP_result/Integron/Other/Integron_structure/': No such file or directory
cat: 'I-VIP_result/Integron/Other/ORFs/': No such file or directory
cat: 'I-VIP_result/Integron/Other/Integron_seqs/': No such file or directory
cat: 'I-VIP_result/Integron/ClassI/Integrase_seqs/': No such file or directory
cat: 'I-VIP_result/Integron/ClassI/Integron_structure/': No such file or directory
cat: 'I-VIP_result/Integron/ClassI/ORFs/': No such file or directory
cat: 'I-VIP_result/Integron/ClassI/Integron_seqs/': No such file or directory
cat: 'I-VIP_result/Integron/ClassI/Genbank_annotation/': No such file or directory
Finished integron extraction!
Step4 Finished: integron extraction

python /home/harbj019/softwarebins/I-VIP.v1.2.py3/scripts/Integron_annotation.py -i /home/harbj019/softwarebins/I-VIP.v1.2.py3/metas -f .fa --r I-VIP_result --a Y --t 24 --tx None.norm --blastp blastp

blastp -query I-VIP_result/Integron/all.ORFs.fasta -db database/SARG.db.fasta -out I-VIP_result/Integron/all.ORFs.fasta.ARG.blast.txt -outfmt 6 -evalue 1e-5 -num_threads 24
blastp -query I-VIP_result/Integron/all.ORFs.ClassI.fasta -db database/SARG.db.fasta -out I-VIP_result/Integron/all.ORFs.ClassI.fasta.ARG.blast.txt -outfmt 6 -evalue 1e-5 -num_threads 24

blastp -query I-VIP_result/Integron/all.ORFs.fasta -db database/MRG.db.fasta -out I-VIP_result/Integron/all.ORFs.fasta.MRG.blast.txt -outfmt 6 -evalue 1e-5 -num_threads 24
blastp -query I-VIP_result/Integron/all.ORFs.ClassI.fasta -db database/MRG.db.fasta -out I-VIP_result/Integron/all.ORFs.ClassI.fasta.MRG.blast.txt -outfmt 6 -evalue 1e-5 -num_threads 24

Warning: [blastp] Query is Empty!
Warning: [blastp] Query is Empty!
Warning: [blastp] Query is Empty!
Warning: [blastp] Query is Empty!
Step5 Finished: gene cassettes annotation

I have tried to work back through the scripts to find where the issue could be, and while i am ok with python, I am not as good your scripts!!

Here is how i am running the pipeline:

python I-VIP.py -i metas -f .fa --a Y --t 24 --u diamond --tc None --tx None

in the metas folder i have a single metagenome.fa file.

i have all the necessary software in my path as well:
$ whereis diamond
diamond: /usr/local/bin/diamond
$ whereis prodigal
prodigal: /home/harbj019/miniconda3/envs/bioinfo/bin/prodigal
$ whereis blastp
blastp: /home/harbj019/miniconda3/envs/bioinfo/bin/blastp

any help would be greatly appreciated.

Thank you again for such a great pipeline!

Hi!
I tried I-VIP on a few genomes that all contain antibiotic-resistant genes of interest for me. Unfortunately, the ARG database used by the program (SARG) does not contain some of these genes; thus, the program does not annotate them. Would it be possible to use other databases (like CARD) for the annotation?
Thank you for your help,
Claudèle

Hello, when I run the example data with "python I-VIP.py -i example -f .gbff --ot 1 --g example --a Y --m 1 --t 32 --u diamond --r example/example_output --tc 4,10 --tx taxon.txt 2>err.txt", I got the following problems. could you help me? thank you!

Traceback (most recent call last):
File "/home/chenyiran/chenyiran/hepeng/software/I-VIP.v1.1.py3/scripts/Integron_annotation.py", line 134, in
for line in open(os.path.join('database/' + 'SARG.structure.txt'), 'r'):
File "/home/chenyiran/anaconda2/envs/tormes-1.0/lib/python3.5/codecs.py", line 321, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa1 in position 234: invalid start byte
Traceback (most recent call last):
File "/home/chenyiran/chenyiran/hepeng/software/I-VIP.v1.1.py3/scripts/Visualization.py", line 351, in
for line in open(os.path.join(annotationdir,anno_file),'r'):
FileNotFoundError: [Errno 2] No such file or directory: 'example/example_output/Integron/all.Integron_structure.ClassI.annotated.formated.txt'

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

• scripts/Integron_annotation.py

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you!
-- Arman (armish/blast-patrol)

Hello..I am having the following problem that i can not solve:

File "I-VIP.py", line 130, in
Length.setdefault(str(line).split('\t')[2], float(str(line).split('\t')[2]))
IndexError: list index out of range

I ask you if you can help me...Thanks!!