Hi,
I’m encountering this error as well, but with daa2rma. I’m running this on Ubuntu 16.04LTS. It seems like things run perfectly fine and then it throws that same error message. I’ve previously run daa-meganizer on this same computer (and, actually on the same input files) without issue.
Here’s my script to run the program:
#!/bin/bash
# Script to run MEGAN6 daa2rma on DIAMOND DAA files from
# 20200103_cbai_diamond_blastx Mox job.
# Requires MEGAN mapping files from:
# http://ab.inf.uni-tuebingen.de/data/software/megan6/download/
# Exit script if any command fails
set -e
# Program path
meganizer=/home/sam/programs/megan/tools/daa2rma
# MEGAN mapping files
prot_acc2tax=/home/sam/data/databases/MEGAN/prot_acc2tax-Jul2019X1.abin
acc2interpro=/home/sam/data/databases/MEGAN/acc2interpro-Jul2019X.abin
acc2eggnog=/home/sam/data/databases/MEGAN/acc2eggnog-Jul2019X.abin
## Inititalize arrays
daa_array_R1=()
daa_array_R2=()
# Create array of DAA R1 files
for daa in *R1*.daa
do
daa_array_R1+=("${daa}")
done
# Create array of DAA R2 files
for daa in *R2*.daa
do
daa_array_R2+=("${daa}")
done
## Run daa2rma
# Capture start "time"
start=${SECONDS}
for index in "${!daa_array_R1[@]}"
do
sample_name=$(echo "${daa_array_R1[index]}" | awk -F "_" '{print $1}')
# Run daa2rma with paired option
${meganizer} \
--paired \
--in "${daa_array_R1[index]}" "${daa_array_R2[index]}" \
--acc2taxa ${prot_acc2tax} \
--acc2interpro2go ${acc2interpro} \
--acc2eggnog ${acc2eggnog} \
--out "${sample_name}".daa2rma.rma6 \
2>&1 | tee --append daa2rma_log.txt
done
# Caputure end "time"
end=${SECONDS}
runtime=$((end-start))
# Print MEGANIZER runtime, in seconds
{
echo ""
echo "---------------------"
echo ""
echo "Total runtime was: ${runtime} seconds"
} >> daa2rm_log.txt
And here’re the resulting log/error messages:
Version MEGAN Community Edition (version 6.18.3, built 17 Dec 2019)
Copyright (C) 2019 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Functional classifications to use: EGGNOG, INTERPRO2GO
Loading ncbi.map: 2,175,506
Loading ncbi.tre: 2,175,510
Opening file: /home/sam/data/databases/MEGAN/prot_acc2tax-Jul2019X1.abin
Loading eggnog.map: 30,875
Loading eggnog.tre: 30,986
Opening file: /home/sam/data/databases/MEGAN/acc2eggnog-Jul2019X.abin
Loading interpro2go.map: 13,501
Loading interpro2go.tre: 29,204
Opening file: /home/sam/data/databases/MEGAN/acc2interpro-Jul2019X.abin
In DAA files: 304428_S1_L001_R1_001.blastx.daa, 304428_S1_L001_R2_001.blastx.daa
Output file: 304428.daa2rma.rma6
Classifications: Taxonomy, EGGNOG, INTERPRO2GO
Annotating RMA6 file using EXTENDED mode
Parsing file: 304428_S1_L001_R1_001.blastx.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% Parsing file: 304428_S1_L001_R2_001.blastx.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (15185.5s)
Total reads: 14,024,469
Alignments: 415,509,683
100% (0.0s)
100% (0.2s)
100% (0.1s)
Linking paired reads
Number of pairs: 5,582,393
Binning reads: Initializing...
Initializing binning...
Using paired reads in taxonomic assignment...
Using 'Naive LCA' algorithm for binning: Taxonomy
Using Best-Hit algorithm for binning: EGGNOG
Using Best-Hit algorithm for binning: INTERPRO2GO
Binning reads...
Binning reads: Analyzing alignments
Total reads: 14,024,469
With hits: 14,024,469
Alignments: 415,509,683
Assig. Taxonomy: 14,001,560
Assig. EGGNOG: 4,036,766
Assig. INTERPRO2GO: 9,134,067
Tax. ass. by mate: 13,638
MinSupport set to: 7012
Binning reads: Applying min-support & disabled filter to Taxonomy...
Min-supp. changes: 3,256
Binning reads: Writing classification tables
Numb. Tax. classes: 138
Numb. EGG. classes: 2,005
Numb. INT. classes: 6,398
Binning reads: Syncing
Class. Taxonomy: 138
Class. EGGNOG: 2,005
Class. INTERPRO2GO: 6,398
100% (42954.5s)
Total time: 58153s
Peak memory: 19.7 of 52.4G
Version MEGAN Community Edition (version 6.18.3, built 17 Dec 2019)
Copyright (C) 2019 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Functional classifications to use: EGGNOG, INTERPRO2GO
Loading ncbi.map: 2,175,506
Loading ncbi.tre: 2,175,510
Opening file: /home/sam/data/databases/MEGAN/prot_acc2tax-Jul2019X1.abin
Loading eggnog.map: 30,875
Loading eggnog.tre: 30,986
Opening file: /home/sam/data/databases/MEGAN/acc2eggnog-Jul2019X.abin
Loading interpro2go.map: 13,501
Loading interpro2go.tre: 29,204
Opening file: /home/sam/data/databases/MEGAN/acc2interpro-Jul2019X.abin
In DAA files: 304428_S1_L002_R1_001.blastx.daa, 304428_S1_L002_R2_001.blastx.daa
Output file: 304428.daa2rma.rma6
Classifications: Taxonomy, EGGNOG, INTERPRO2GO
Annotating RMA6 file using EXTENDED mode
Parsing file: 304428_S1_L002_R1_001.blastx.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% Parsing file: 304428_S1_L002_R2_001.blastx.daa
10% 20% 30% 40% 50% 60% 70% 80% 90% 100% (15334.9s)
Total reads: 13,559,260
Alignments: 402,164,513
100% (0.0s)
100% (0.1s)
100% (0.1s)
Linking paired reads
Number of pairs: 5,391,268
Binning reads: Initializing...
Initializing binning...
Using paired reads in taxonomic assignment...
Using 'Naive LCA' algorithm for binning: Taxonomy
Using Best-Hit algorithm for binning: EGGNOG
Using Best-Hit algorithm for binning: INTERPRO2GO
Binning reads...
Binning reads: Analyzing alignments
Version MEGAN Community Edition (version 6.18.3, built 17 Dec 2019)
Copyright (C) 2019 Daniel H. Huson. This program comes with ABSOLUTELY NO WARRANTY.
Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using 'localhost:10.0' as the value of the DISPLAY variable.
at java.desktop/sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
at java.desktop/sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:102)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:61)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:315)
at java.desktop/java.awt.GraphicsEnvironment$LocalGE.createGE(GraphicsEnvironment.java:101)
at java.desktop/java.awt.GraphicsEnvironment$LocalGE.<clinit>(GraphicsEnvironment.java:83)
at java.desktop/java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:129)
at java.desktop/sun.awt.X11.XToolkit.<clinit>(XToolkit.java:232)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:315)
at java.desktop/java.awt.Toolkit$2.run(Toolkit.java:588)
at java.desktop/java.awt.Toolkit$2.run(Toolkit.java:583)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.desktop/java.awt.Toolkit.getDefaultToolkit(Toolkit.java:582)
at java.desktop/java.awt.Component.getToolkitImpl(Component.java:1249)
at java.desktop/java.awt.Component.getToolkit(Component.java:1237)
at java.desktop/java.awt.Component.checkImage(Component.java:3835)
at java.desktop/java.awt.ImageMediaEntry.getStatus(MediaTracker.java:953)
at java.desktop/java.awt.MediaTracker.statusID(MediaTracker.java:717)
at java.desktop/java.awt.MediaTracker.waitForID(MediaTracker.java:665)
at java.desktop/javax.swing.ImageIcon.loadImage(ImageIcon.java:314)
at java.desktop/javax.swing.ImageIcon.<init>(ImageIcon.java:244)
at jloda/jloda.swing.util.ResourceManager.getIcon(ResourceManager.java:62)
at jloda/jloda.swing.util.ResourceManager.getIcons(ResourceManager.java:81)
at megan/megan.main.MeganProperties.initializeProperties(MeganProperties.java:101)
at megan/megan.tools.DAA2RMA6.run(DAA2RMA6.java:175)
at megan/megan.tools.DAA2RMA6.main(DAA2RMA6.java:67)