Centers for Disease Control and Prevention
Question
Asked 24th May, 2017
Help with NCBI table2asn
Does anyone have experience with the table2asn tool of NCBI? It is used for submitting annotations of genomes using GFF files.
It can be found at this location: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/table2asn_GFF/
I am having a problem with it.
1) The windows tool I get running, but it gives me an error. The command used is the following: table2asn -M n -J -c w -t template.sbt -a r10k -l paired-ends -i FinalContigs.fsa -f 2700988623.gff -o output_file.sqn -Z output_file.dr -locus-tag-prefix xxxxx
template.sbt is a file generated by NCBI
FinalContigs.fsa is a file containing all the different contigs of the draft genome. The first contig is named Contig001, seconf contig is Contig002, and so on.
2700988623.gffis the file containing the annotation. Column 1 gives the contigs where the CDS and RNA are found in, so Contig001, Contig002, etc.
After running the command (as told by NCBI), I get the following error:
Cannot resolve lcl|Contig002: unknown
Line: 0
So if anyone could assist me with getting the tool running in Windows, that would be very much appreciated as it is the final step of submitting my genome.
Thanks in advance!
Most recent answer
Muhammad Arslan This is like 4 years late but maybe it gets found by someone in the future and can serve as a record. I tried the tool on all three OSs and the same problem persisted. However, it is not that chmod +x does not work, it is that after it is run it is really hard for the terminal to see the file and run it. In all three cases, this is overcome by adding the path to the file in front of its name as you run it. So, for example, instead of running
table2asn -M n -J -c w -euk -t...
You would add in the path and run
/Path/to/thefile/table2asn -M n -J -c w -euk -t....
Easiest way to know wha the exact path is is to just drag and drop the file into the terminal window and the terminal will tell you
Furthermore, to be more explicit, the exact steps to get this tool to run are:
1) Download it, unzip it (on Linux, or Ubuntu on PC or equivalent) you run "unzip NameOfFile" and you may have to install unzip first via "sudo apt-get install unzip"
2) Run chmod +x on the unzipped file. I did confirm that at this stage, you can rename the file to whatever you want, such as instead of "linux64.table2asn" you can just name it table2asn (I think the full name will be table2asn.table2asn but you can call it up with just table2asn)
3) Ru it with the path, or if you know what you are doing, you can add the file to the path and then it will run with just "table2asn" instead of needing to include the path. However, and this was so confusing to me, even if your terminal is in the same directory that the table2asn file is in it will still not see it and call it up, so I am not 100% sure if the "adding to path" route would fix the issue; I didn't try it yet
Anyways, for anyone searching the web for how to get this to work, there's the steps. A more comprehensive README if you will. As for all the options and tools, I haven't actually run this successfully yet (need to specify locus-tags apparently) so I cannot comment about the options yet
All Answers (5)
University of Copenhagen
Hi, have you seen if the header is the same (.fsa and .gff)? Looks like the error msg is talking about it: your .fsa is Contig002 and the GFF lcl|Contig002.
Usually when I send the genome to Genbank I prefer to use the table2asn with the tbl format.
You should convert the GFF into TBL before using the table2asn.
You can use this tool: https://genomeannotation.github.io/GAG/
gag.py --fasta organism.fasta --gff organism.gff --out gag_output (tbl)
When you convert the GFF to TBL the probability of error is reduced.
Wageningen University & Research
Thank you Juliana for your reply!
In the meanwhile I have tried to use the GAG script, but somehow something goes wrong. The gff table is completely ok, since it gives no errors at NCBI when running their scripts, but when I use it as input for the GAG tool, it somehow does not detect the CDS features.
To give you an idea of how the file looks, I have attached part of it here. Maybe you can see what went wrong?
University of Copenhagen
Hi!
Your file is missing the mRNA and Exon feature.
You can add the mRNA feature
##gff-version 3 ##gff-version 3
University of Alberta
Hi Guillaume,
I am trying to run the tool but unable to do so. How did you install it? chmod +x doesn't work for me. Can you please comment. Thanks
Arslan
Centers for Disease Control and Prevention
Muhammad Arslan This is like 4 years late but maybe it gets found by someone in the future and can serve as a record. I tried the tool on all three OSs and the same problem persisted. However, it is not that chmod +x does not work, it is that after it is run it is really hard for the terminal to see the file and run it. In all three cases, this is overcome by adding the path to the file in front of its name as you run it. So, for example, instead of running
table2asn -M n -J -c w -euk -t...
You would add in the path and run
/Path/to/thefile/table2asn -M n -J -c w -euk -t....
Easiest way to know wha the exact path is is to just drag and drop the file into the terminal window and the terminal will tell you
Furthermore, to be more explicit, the exact steps to get this tool to run are:
1) Download it, unzip it (on Linux, or Ubuntu on PC or equivalent) you run "unzip NameOfFile" and you may have to install unzip first via "sudo apt-get install unzip"
2) Run chmod +x on the unzipped file. I did confirm that at this stage, you can rename the file to whatever you want, such as instead of "linux64.table2asn" you can just name it table2asn (I think the full name will be table2asn.table2asn but you can call it up with just table2asn)
3) Ru it with the path, or if you know what you are doing, you can add the file to the path and then it will run with just "table2asn" instead of needing to include the path. However, and this was so confusing to me, even if your terminal is in the same directory that the table2asn file is in it will still not see it and call it up, so I am not 100% sure if the "adding to path" route would fix the issue; I didn't try it yet
Anyways, for anyone searching the web for how to get this to work, there's the steps. A more comprehensive README if you will. As for all the options and tools, I haven't actually run this successfully yet (need to specify locus-tags apparently) so I cannot comment about the options yet
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