igv tools error

[Jay Mie Kua]

Hi, 

I am trying to convert bam files to tdf file using igvtools at command line, but i am getting this error. 

Using system JDK.

WARN [2024-06-27T16:28:15,113]  [Globals.java:138] [main]  Development mode is enabled

INFO [2024-06-27T16:28:15,121]  [IgvTools.java:838] [main]  Computing coverage.  File = /home/<file>.sorted.bam

Computing coverage.  File = /home/<file>.sorted.bam

INFO [2024-06-27T16:28:15,122]  [IgvTools.java:839] [main]  Max zoom = 5

Max zoom = 5

INFO [2024-06-27T16:28:15,122]  [IgvTools.java:840] [main]  Window size = 10

Window size = 10

INFO [2024-06-27T16:28:15,126]  [IgvTools.java:845] [main]  Window functions: mean

Window functions: mean

INFO [2024-06-27T16:28:15,126]  [IgvTools.java:846] [main]  Ext factor = 0

Ext factor = 0

INFO [2024-06-27T16:28:15,152]  [DirectoryManager.java:179] [main]  IGV Directory: /home/igv

IGV Directory: /home/igv

INFO [2024-06-27T16:28:15,152]  [GenomeManager.java:195] [main]  Loading genome: /home/Arabidopsis_thaliana.TAIR10.dna.toplevel.genome

Loading genome: /home/Arabidopsis_thaliana.TAIR10.dna.toplevel.genome

ERROR [2024-06-27T16:28:15,160]  [IgvTools.java:260] [main]  Unexpected IO error:

org.broad.igv.tools.PreprocessingException: Unexpected IO error:

        at org.broad.igv.tools.IgvTools.run(IgvTools.java:484) ~[igv.jar:?]

        at org.broad.igv.tools.IgvTools.main(IgvTools.java:255) [igv.jar:?]

Caused by: java.util.zip.ZipException: zip END header not found

        at java.util.zip.ZipFile$Source.zerror(ZipFile.java:1567) ~[?:?]

        at java.util.zip.ZipFile$Source.findEND(ZipFile.java:1462) ~[?:?]

        at java.util.zip.ZipFile$Source.initCEN(ZipFile.java:1469) ~[?:?]

        at java.util.zip.ZipFile$Source.<init>(ZipFile.java:1274) ~[?:?]

        at java.util.zip.ZipFile$Source.get(ZipFile.java:1237) ~[?:?]

        at java.util.zip.ZipFile$CleanableResource.<init>(ZipFile.java:727) ~[?:?]

        at java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:844) ~[?:?]

        at java.util.zip.ZipFile.<init>(ZipFile.java:247) ~[?:?]

        at java.util.zip.ZipFile.<init>(ZipFile.java:177) ~[?:?]

        at java.util.zip.ZipFile.<init>(ZipFile.java:191) ~[?:?]

        at org.broad.igv.feature.genome.GenomeManager.parseGenomeArchiveFile(GenomeManager.java:761) ~[igv.jar:?]

        at org.broad.igv.feature.genome.GenomeManager.loadDotGenomeFile(GenomeManager.java:507) ~[igv.jar:?]

        at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:216) ~[igv.jar:?]

        at org.broad.igv.tools.IgvTools.loadGenome(IgvTools.java:1192) ~[igv.jar:?]

        at org.broad.igv.tools.IgvTools.doCount(IgvTools.java:849) ~[igv.jar:?]

        at org.broad.igv.tools.IgvTools.run(IgvTools.java:372) ~[igv.jar:?]

        ... 1 more

Unexpected IO error:

org.broad.igv.tools.PreprocessingException: Unexpected IO error:

        at org.broad.igv.tools.IgvTools.run(IgvTools.java:484) ~[igv.jar:?]

        at org.broad.igv.tools.IgvTools.main(IgvTools.java:255) [igv.jar:?]

Caused by: java.util.zip.ZipException: zip END header not found

        at java.util.zip.ZipFile$Source.zerror(ZipFile.java:1567) ~[?:?]

        at java.util.zip.ZipFile$Source.findEND(ZipFile.java:1462) ~[?:?]

        at java.util.zip.ZipFile$Source.initCEN(ZipFile.java:1469) ~[?:?]

        at java.util.zip.ZipFile$Source.<init>(ZipFile.java:1274) ~[?:?]

        at java.util.zip.ZipFile$Source.get(ZipFile.java:1237) ~[?:?]

        at java.util.zip.ZipFile$CleanableResource.<init>(ZipFile.java:727) ~[?:?]

        at java.util.zip.ZipFile$CleanableResource.get(ZipFile.java:844) ~[?:?]

        at java.util.zip.ZipFile.<init>(ZipFile.java:247) ~[?:?]

        at java.util.zip.ZipFile.<init>(ZipFile.java:177) ~[?:?]

        at java.util.zip.ZipFile.<init>(ZipFile.java:191) ~[?:?]

        at org.broad.igv.feature.genome.GenomeManager.parseGenomeArchiveFile(GenomeManager.java:761) ~[igv.jar:?]

        at org.broad.igv.feature.genome.GenomeManager.loadDotGenomeFile(GenomeManager.java:507) ~[igv.jar:?]

        at org.broad.igv.feature.genome.GenomeManager.loadGenome(GenomeManager.java:216) ~[igv.jar:?]

        at org.broad.igv.tools.IgvTools.loadGenome(IgvTools.java:1192) ~[igv.jar:?]

        at org.broad.igv.tools.IgvTools.doCount(IgvTools.java:849) ~[igv.jar:?]

        at org.broad.igv.tools.IgvTools.run(IgvTools.java:372) ~[igv.jar:?]

        ... 1 more

This is how my .genome file looks like: 

name: Arabidopsis_thaliana_TAIR10
id: Arabidopsis_thaliana_TAIR10
fasta: /home/jaymie/refFiles/genomes/Ensembl50/Ath/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
1 dna:chromosome chromosome:TAIR10:1:1:30427671:1 REF 30427671
2 dna:chromosome chromosome:TAIR10:2:1:19698289:1 REF 19698289
3 dna:chromosome chromosome:TAIR10:3:1:23459830:1 REF 23459830
4 dna:chromosome chromosome:TAIR10:4:1:18585056:1 REF 18585056
5 dna:chromosome chromosome:TAIR10:5:1:26975502:1 REF 26975502
Mt dna:chromosome chromosome:TAIR10:Mt:1:366924:1 REF 366924
Pt dna:chromosome chromosome:TAIR10:Pt:1:154478:1 REF 154478

Thanks, 

Jaymie

[igv-help]

How did you create the ".genome" file?   

[Jay Mie Kua]

this is my code: 

#!/bin/bash

# Define the path to your FASTA file
FASTA_FILE="/<path>/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa"

# Define the path to your genome file
GENOME_FILE="/<path./Arabidopsis_thaliana.TAIR10.dna.toplevel.genome"

# Create the .genome file header
echo "name: Arabidopsis_thaliana_TAIR10" > "$GENOME_FILE"
echo "id: Arabidopsis_thaliana_TAIR10" >> "$GENOME_FILE"
echo "fasta: $FASTA_FILE" >> "$GENOME_FILE"

# Extract chromosome names and lengths and append to the .genome file
awk '/^>/{if (seqlen){print chrom "\tdna:chromosome chromosome:TAIR10:" chrom ":1:" seqlen ":1 REF\t" seqlen}; chrom=substr($0, 2); seqlen=0; next; }{ seqlen += length($0)}END{print chrom "\tdna:chromosome chromosome:TAIR10:" chrom ":1:" seqlen}' "$FASTA_FILE" >> "$GENOME_FILE"

# Display the genome file content
echo "Genome file content:"
cat "$GENOME_FILE"

# Verify the FASTA file exists
if [ -f "$FASTA_FILE" ]; then
    echo "FASTA file found: $FASTA_FILE"
else
    echo "FASTA file not found: $FASTA_FILE"
    exit 1
fi

# Check chromosome headers in the FASTA file
echo "Chromosome headers in FASTA file:"
grep ">" "$FASTA_FILE"

[James Robinson]

That is not a ".genome" file,  I'm not sure what it is.    

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[James Robinson]

I suggest you use the "chrom.sizes" option, it's just a tab delimited 2 column file mapping sequence name to length.   See the igvtools readme.