Error: The genome [PAO1 genome (my created genome)] cannot be read. Would you like to remove...

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A Lippa

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Dec 3, 2017, 9:17:15 PM12/3/17
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I cannot import a new genome from a fasta and .gff file for Pseudomonas aeruginosa PAO1.

If posting about a problem, please include:
  1. The version of IGV you are using, and your computer operating system: IGV 2.4.4, Windows 7 professional
  2. What you did. If the problem happens when you open a file and/or view certain genomic coordinates, attach the file* (or provide a link) and specify the genomic coordinates. Please DO NOT paste the contents of your file into an email or in the group's web interface, as files are whitespace sensitive which gets lost when sent in the body of an email. (see https://drive.google.com/drive/folders/1RviBz-jZzmu3kgJz3x9FL6gYUfaQsMwo?usp=sharing)

           When I click on "Genomes"->"Create .genome file"->enter name of database, descriptor (PAO1 genome, PAO1 genome, respectively), fasta file (PAO1.fna), and gene file (PAO1.gff), the latter two from NCBI. I save the file to a directory and then the program returns the error " The genome [PAO1 genome] cannot be read. Would you like to remove the selected entry?"
The .genome file is still written but will not load.


3. What you expected to happen: Program should load the imported genome file after creating it
4. What actually happened: Error listed above

5. Your igv.log file. It will be in <your home directory>/igv--there is no such file in that directory.


Your help is much appreciated, as I had someone else produce a genome for me, but I received other errors when using the genome she created.


Sincerely,

Andrew

James Robinson

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Dec 3, 2017, 10:59:37 PM12/3/17
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Is your fasta file indexed?  I do not see a ".fai" file in your data folder.   This is required.

However, stepping back why are you creating a .genome file?  It is far simpler to just load the fasta as your reference,  the load tracks (such as your gff) from the file menu.   The .genome file is only needed for a few special circumstances,  for example to include a cytobad ideogram file.      

If you use the fasta as your genome reference it will create the index automatically if it doesn't exist.    If you continue to have issues please include your igv.log file,  in your igv folder under your home directory.

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A Lippa

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Dec 4, 2017, 10:13:04 AM12/4/17
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There is no Ihab.log file on the computer or in that directory—I searched. 

Yes, the file was indexed, but that didn’t solve the problem. Besides, according to your webpage on how to import a genome, IGV indexes the fasts file automatically, which is why it needs to be in a folder that allows writing permissions (and, indeed, if the index files are deleted, the program does generate them.). 

I need to create alignments between the genome file with annotations from the gff file with a wig file dataset. Are you saying that I can do this without importing/ creating a genome?

Thanks,
Andrew 

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James Robinson

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Dec 4, 2017, 2:14:51 PM12/4/17
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The filename is igv.log,  not ihab.log.   

Creating a .genome file is not neccessary.   Sorry our documentation is not clear about that,  we will correct that.   Just load the fasta to define the genome  (Genomes > Load genome from file > select fasta).    You can load any number of annotation files (e..g gff) after that from the file menu.    When using this option the .fasta file will be automatically indexed.



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A Lippa

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Dec 4, 2017, 3:14:32 PM12/4/17
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Sorry, I am writing from a phone with a hand splint and the file name was a typo. There is no igv.log file I the folder or on the computer by file search. 

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James Robinson

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Dec 4, 2017, 5:05:18 PM12/4/17
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What version of igv are you using?   Did you find the igv folder,  it should be in your home directory.    What are the contents of this folder?

I only need the igv.log to determine what the problem might be with the .genome file,  but as we've discussed the .genome file is not necessary and not even recommended.  

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A Lippa

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Dec 6, 2017, 12:18:16 PM12/6/17
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Hi James,
IVG 2.4.4, I unzipped to my desktop (I'm a PC user as noted in the original post, so there is no "home.") and there is no igv.log file (see photo).

I did solve the problem by just loading the fasta and gff files separately. Thanks.

Andrew

Inline image 1

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Andrew M. Lippa, MD, PhD
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James Robinson

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Dec 6, 2017, 12:35:10 PM12/6/17
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Glad you solved your problem.  I clarified the doc to steer people more strongly in that direction.   Although its mute now,  the .genome file you sent would fail if the fasta and annotation file were in a separate folder.

BTW, for the future the igv.log file is not in the zipped folder you downloaded,  its in a separate "igv" folder under your home directory,  by home I mean user home directory.   Its literally impossible for IGV to startup without creating an igv.log file.   

Best,

Jim

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A Lippa

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Dec 6, 2017, 1:46:07 PM12/6/17
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Now I understand. It is in the user home directory and is attached (not sure why Explorer search didn't find it).
The fasta and GFF file were in the same folder as the .genome file I sent you.

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igv.log

James Robinson

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Dec 6, 2017, 2:06:27 PM12/6/17
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OK, thanks.   The specific error is it can't find the following file:

C:\Users\Andrew M Lippa\Documents\Dove Lab\Dropbox\for Andrew\PAO1.fna.fai

I think you indicated that it does exist though.  In any event defining the reference with the fasta and loading annotations separately is a better solution.

Jim


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A Lippa

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Dec 6, 2017, 2:51:09 PM12/6/17
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Sounds good. Yeah, it gave that error when a friend sent me her .genome file to use on dropbox. Despite creating a folder (the path really didn't exist) that had the path with the .fna.fai file in it, it didn't give the error, but it didn't load either.

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Blaise Li

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Apr 25, 2018, 7:00:21 AM4/25/18
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Dear IGV people, I have a similar issue, but on linux, with a locally-created .genome file.

I tried to create a .genome file from a fasta file and the creation fails, with the IGV output looking as follows:

WARN [2018-04-25 11:39:52,090]  [Globals.java:138] [AWT-EventQueue-0]  Development mode is enabled
INFO [2018-04-25 11:39:52,128]  [DirectoryManager.java:171] [AWT-EventQueue-0]  IGV Directory: /home/bli/igv
INFO [2018-04-25 11:39:52,128] [DirectoryManager.java:171]  IGV Directory: /home/bli/igv
INFO [2018-04-25 11:39:52,130]  [Main.java:154] [AWT-EventQueue-0]  Startup  IGV Version 2.4.10 03/20/2018 10:50 PM
INFO [2018-04-25 11:39:52,131]  [Main.java:155] [AWT-EventQueue-0]  Java 1.8.0_162
INFO [2018-04-25 11:39:52,131]  [DirectoryManager.java:76] [AWT-EventQueue-0]  Fetching user directory...
INFO [2018-04-25 11:39:52,153]  [Main.java:156] [AWT-EventQueue-0]  Default User Directory: /home/bli
INFO [2018-04-25 11:39:52,153]  [Main.java:157] [AWT-EventQueue-0]  OS: Linux


Apr 25, 2018 11:39:52 AM java.util.prefs.FileSystemPreferences$6 run
WARNING: Prefs file removed in background /home/bli/.java/.userPrefs/prefs.xml
INFO [2018-04-25 11:40:03,283]  [GenomeManager.java:186] [pool-2-thread-1]  Loading genome: /home/bli/igv/genomes/ce11.genome
INFO [2018-04-25 11:41:36,180]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box
INFO [2018-04-25 11:41:36,181]  [IGVCommandBar.java:165] [AWT-EventQueue-0]  Selecting genome WBcel235_mCherry
INFO [2018-04-25 11:41:36,183]  [GenomeComboBox.java:79] [AWT-EventQueue-0]  Enter genome combo box
INFO [2018-04-25 11:41:36,184]  [GenomeComboBox.java:85] [AWT-EventQueue-0]  Loading C. elegans with mCherry transcript as an extra chromosome
INFO [2018-04-25 11:41:36,186]  [GenomeComboBox.java:96] [pool-2-thread-2]  Loading WBcel235_mCherry
INFO [2018-04-25 11:41:36,275]  [GenomeManager.java:186] [pool-2-thread-2]  Loading genome: /Genomes/C_elegans/WBcel235_mCherry.genome
ERROR [2018-04-25 11:41:36,296]  [GenomeComboBox.java:117] [pool-2-thread-2]  java.io.FileNotFoundException: /extra/pasteur/entites/Mhe/Genomes/C_elegans/WBcel235_mCherry.fa.fai (No such file or directory)
INFO [2018-04-25 11:41:39,131]  [GenomeComboBox.java:79] [pool-2-thread-2]  Enter genome combo box
ERROR [2018-04-25 11:41:39,132]  [GenomeComboBox.java:126] [pool-2-thread-2]  Error initializing genome
java.io.FileNotFoundException: /extra/pasteur/entites/Mhe/Genomes/C_elegans/WBcel235_mCherry.fa.fai (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:118)
    at org.broad.igv.util.ParsingUtils.openInputStream(ParsingUtils.java:96)
    at org.broad.igv.util.ParsingUtils.openBufferedReader(ParsingUtils.java:78)
    at org.broad.igv.feature.genome.fasta.FastaIndex.parseIndexFile(FastaIndex.java:89)
    at org.broad.igv.feature.genome.fasta.FastaIndex.<init>(FastaIndex.java:55)
    at org.broad.igv.feature.genome.fasta.FastaIndexedSequence.<init>(FastaIndexedSequence.java:67)
    at org.broad.igv.feature.genome.fasta.FastaIndexedSequence.<init>(FastaIndexedSequence.java:57)
    at org.broad.igv.feature.genome.GenomeManager.loadDotGenomeFile(GenomeManager.java:525)
    at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:206)
    at org.broad.igv.ui.commandbar.GenomeComboBox$GenomeBoxActionListener$1.run(GenomeComboBox.java:110)
    at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)


It seems that IGV is constructing an erroneous non-existing path for the .fa.fai file. I suspect this may be related with difficulties handling symbolic links: the /extra/pasteur directory does not exist. The real path to the directory containing the fasta file and its index is /extra/Genomes/C_elegans/ but I loaded it by giving a path containing some symbolic links.
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