Activity for PhageTerm
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Olivia Dutton posted a comment on discussion General Discussion
Hiya, I am trying to run the following command in my Jupyter notebook... !/shared/team/Liv_D/phageterm_source/ptv-py3_release_1_light/PhageTerm.py -f /shared/team/Liv_D/TestFullAssemblyNewPhage/275341_BcenoNewphage1_1_trimmed.fastq -p /shared/team/Liv_D/TestFullAssemblyNewPhage/275341_BcenoNewphage1_2_trimmed.fastq -r /shared/team/Liv_D/TestFullAssemblyNewPhage/phage1_pilonR1/pilon.fasta --report_title putative_phage But am getting the following error.... Unrecognized test run argument ('None')!...
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Julian Garneau posted a comment on discussion General Discussion
Hello Ruby, thanks for your message, If you aggree, could you send me your PhageTerm report, so I can have a look at the coverage on your assembly? PhageTerm has been developed and tested for randomly sheared short reads. We haven't tested officially with long reads, so we can't be sure that it will work or not. In principle , if the quantity of reads starting at the termini is really high, and reads starting randomly over the genome is well distributed everywhere on the genome, we expect phageterm...
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Ruby Setiawan posted a comment on discussion General Discussion
Hi, I have a phage genome that I assembles from ONT and I only have this long read sequencing. Later, I also try installing PhageTerm refer to this link, and I ran the PhageTerm using the assembled genome and raw reads from ONT and I got a warning WARNING: average coverage is under the limit of the software (50) I also check my assembly log and I have a coverage more than 500x for that assembled genome. Do you have any suggestion on how to use PhageTerm for long-read assembled genome?
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Melissa Walker posted a comment on discussion General Discussion
Julian, I will send you a copy straight away. Your help is truly appreciated.
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Hi Melissa, thanks for your message, It is hard for me to give a decisive answer on this case, but yes, PhageTerm is usually conservative and will not suggest the re-organization it there is an uncertainty with multiple termini. I would have to look at the report to have a better idea of what is happening there... If you want to send me your report I can have a look: julian.garneau@unil.ch Cheers, Julian
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Hello, thanks for your message, You have a phage genome from ONT, are you talking about the assembly? Do you have short reads from Illumina sequencing or you only have long read from ONT sequencing? Thank you
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Hello, I have run the PhageTerm.py script and am getting an empty re-ordered .fasta file. I am unsure of how to troubleshoot this issue. My phageterm pdf file indicates that there are multiple preferential termini on the forward strand and one obvious termini on the reverse strand. My thought is that the presence of multiple termini make it hard for the program to choose one by which to re-order. If this is the case, is there a way by which I can have the program do this? My line of code is: ptv-py3_release_1/PhageTerm.py...
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Hi, I have a problem when running PhageTerm. I have a phage genome from long-read sequencing (ONT). When I run the script, I got an error message as: ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (2,) + inhomogeneous part. Do you have any idea what causing this error? And what solution I could try to fix the error? Thank you
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Hi again Concha, Could you send me an e-mail at julian.garneau@pasteur.fr WIll be easier to exchange on there, Thanks!
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Concha Eloko Robby posted a comment on discussion General Discussion
Hi again, Thanks for your quick answer. Before receiving it, I tried using the Maximilian Press 's version compatible with python3. The process went until the end, i.e without any error messages but I reckon some of the outputs were incorrect : the corrected fasta was empty for all the tested phages (~70). However, I got some seemingly good reports : I compared one of them with one obtained on the galaxy platform of the institute and they were identical. However I am still very interested in the...
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Bonsoir :) When you run the installation test, could try without your own reads, as follow : $ /home/user/software/phageterm-1.0.12/PhageTerm.py -t C5 Tell me if this command works properly on your system. If not, maybe you should force launching phageterm with python2 : $ python2 PhageTerm.py -t C5 And with your own reads : $ python2 PhageTerm.py -f K10PH82C1_S15_R1_001.fastq -p K10PH82C1_S15_R2_001.fastq -r K10PH82C1_sequence.fasta -n K10PH82C1 -c 4 Keep me posted if it worked with one of those...
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Bonjour ! I tried running the script on a recently sequenced phage. The input are paired reads, the command line is as follow : /home/user/software/phageterm-1.0.12/PhageTerm.py -f K10PH82C1_S15_R1_001.fastq -p K10PH82C1_S15_R2_001.fastq -r K10PH82C1_sequence.fasta -n K10PH82C1 -t installation_test -c 4 After calculating coverage values until 100%, I get the following error message : AttributeError: 'module' object has no attribute 'VERSION' identity=[ImageReader@0x7f6515c8c8d0 I tried running the...
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Hello, Please tell me more about the results. What type of phage have you got in the PDF report? I ask because a fasta file is not generated for all types of phage. (If your phage is type T4 with no precise termini, we cant generate a fasta file reorganized to start at the termini because there is no termini). So the absence of a fasta file is not necessarily a bug. But I need more info to know if its a bug here or not. Thank you :)
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Jedrzej posted a comment on discussion General Discussion
Hello! I am trying to use phageterm, but only output i got were .pdf report and .csv statistics. No fasta file. There were no errors. I used 2 paired fastq.gz files and valid contig for -r. Any ideas what could go wrong? Thank you in advance
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Hi Gustavo, thanks for the details, I forgot to ask you, what procedure did you use to sequence your phage? Did you do illumina TruSeq libraries? Nextera? Other? For further communications, do you mind writing me on my email ? This will be faster and easier :) At: julian.garneau@pasteur.fr
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Gustavo Teixeira posted a comment on discussion General Discussion
Hello Julian, I've attached some of the output files generated by PhagTerm on my latest run. I used RAST on both assemblies, the bigger one contained new and different CDSs when compared to the smaller sequence generated by PhageTerm. One of the main differences was the RNA content, which the smaller sequence seemed to have none, according to RAST. Also the bigger sequence contained three CDSs identified on the Ribonucleotide reduction subsystem that were'nt present on the PhageTerm output. It seems...
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Hi again Gustavo, Can you help me by telling me what is the result you obtained on that contig after the PhageTerm analysis? That should help me help you. Only thing I can guess for now, is that your result is possibly a "DTR-long" , and that the repeat region was taken out of the reorganised genome. However, since there is a 21 503 difference between both contigs, that seems pretty big for a DTR, which I think at maximum have been seen at around 10 000 bp. But that is not impossible. Anyway, I will...
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Hello there Recently I started using PhageTerm on my phage genomes, altough only after some time I noticed that the size of the new contig (83866) created was subtabtially smaller than the inputed contig (105369) Why the software decreased the size of my contig? How can this be fixed? Thank you in advance
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Thank you it worked!!
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Hi Gustavo, You can actually use the option -p for the second paired-end read file, as mentioned in the READ_ME. So you would have someting like this : -f forward.fastq -p reverse.fastq Hope this helps Options: Raw reads file in fastq format: -f INPUT_FILE, --fastq=INPUT_FILE Fastq reads (NGS sequences from random fragmentation DNA only, e.g. Illumina TruSeq) Raw reads file in fastq format: -p INPUT_FILE, --paired=INPUT_FILE Paired fastq reads
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sorry wrong post
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Hello there I'm having trouble running the program Calculating coverage values, please wait (may take a while)... If your computer has more than 1 processor, you can use the -c or --core option to speed up the process. 100.0 %ERROR: No read Match, please check your fastq file Finished calculating coverage values, the remainder should be completed rapidly Traceback (most recent call last): File "/home/gustavo/Documentos/00_Softwares/phageterm-1.0.12/PhageTerm.py", line 288, in <module> termini_coverage...
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Monot posted a comment on discussion General Discussion
Dear Patricia, This mean that you launch with python3, PhageTerm is coded in Python 2 version I recommend using at least Python 2.7. Best, Marc
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nabisubi patricia posted a comment on discussion General Discussion
print "\nPerforming a test run using test phage sequence with 5 prime cohesive overhang :" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("\nPerforming a test run using test phage sequence with 5 prime cohesive overhang :")?
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PhageTerm released /README.txt
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