[2026-06-02 20:58:07] [miniwdl-eks.task] Staging: downloading command and 3 inputs
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/command /tmp/miniwdl_task/command
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/3c/3c95c4f402854c7353671c201c10e77e/work/3599996130_r7__chr1_207752171_C_T.igv_script.txt /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7__chr1_207752171_C_T.igv_script.txt
cp s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20260129_LH00519_0054_A23JHYNLT4/1076-add-custom-fastq-sample-merging_afd6c9_260203104147/bams/3599996130_r7.bam.bai /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam.bai
cp s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20260129_LH00519_0054_A23JHYNLT4/1076-add-custom-fastq-sample-merging_afd6c9_260203104147/bams/3599996130_r7.bam /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam
[2026-06-02 20:58:33] [miniwdl-eks.task] Staging completed (3 inputs, 26899ms) s5cmd=workers:256,concurrency:10,cpus:24
+ BAM_TOKEN=/tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam
+ INDEX_TOKEN=/tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam.bai
+ mkdir 3599996130_r7__chr1_207752171_C_T
+ sed 's|::BAM_FILE::|/tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam index=/tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam.bai|g' /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7__chr1_207752171_C_T.igv_script.txt
+ XVFB_PID=111
+ DISPLAY=:2
+ /igv/jdk-11/bin/java --module-path=/igv/lib -Xmx5g @/igv/igv.args --module=org.igv/org.broad.igv.ui.Main -b 3599996130_r7__chr1_207752171_C_T/igv_batch_script.txt
+ Xvfb :2
WARNING: package com.sun.java.swing.plaf.windows not in java.desktop
WARNING: package sun.awt.windows not in java.desktop
INFO [Jun 02,2026 20:58] [Globals] Development mode is enabled
Jun 02, 2026 8:58:34 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
INFO [Jun 02,2026 20:58] [Main] Startup  IGV Version 2.16.0 01/25/2023 01:50 PM
INFO [Jun 02,2026 20:58] [Main] Java 11.0.13 (build 11.0.13+8) 2021-10-19
INFO [Jun 02,2026 20:58] [Main] Java Vendor: Eclipse Adoptium https://adoptium.net/
INFO [Jun 02,2026 20:58] [Main] JVM: OpenJDK 64-Bit Server VM Temurin-11.0.13+8   
INFO [Jun 02,2026 20:58] [Main] OS: Linux 6.12.83 amd64
INFO [Jun 02,2026 20:58] [Main] IGV Directory: /root/igv
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO [Jun 02,2026 20:58] [AmazonUtils] AWS default credentials found. AWS support enabled.
INFO [Jun 02,2026 20:58] [CommandListener] Listening on port 60151
INFO [Jun 02,2026 20:58] [BatchRunner] Executing batch script: 3599996130_r7__chr1_207752171_C_T/igv_batch_script.txt
INFO [Jun 02,2026 20:58] [GenomeManager] Loading genome: https://s3.amazonaws.com/igv.org.genomes/hg19/hg19.json
INFO [Jun 02,2026 20:58] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz
INFO [Jun 02,2026 21:02] [GenomeManager] Loading genome: https://igv.org/genomes/legacy/json/hg38.json
INFO [Jun 02,2026 21:02] [TrackLoader] Loading resource:  https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
INFO [Jun 02,2026 21:03] [TrackLoader] Loading resource:  /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam
WARNING: BAM index file /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam.bai is older than BAM /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam
WARNING: BAM index file /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam.bai is older than BAM /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam
WARNING: BAM index file /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam.bai is older than BAM /tmp/miniwdl_task/work/_miniwdl_inputs/0/3599996130_r7.bam
INFO [Jun 02,2026 21:03] [ShutdownThread] Shutting down
+ kill 111
[2026-06-02 21:03:09] [miniwdl-eks.task] Task finished exit_code=0 (275494ms)
cp /tmp/miniwdl_task/stdout.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/stdout.txt
cp /tmp/miniwdl_task/stderr.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/stderr.txt
cp work/3599996130_r7__chr1_207752171_C_T/igv_batch_script.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/work/3599996130_r7__chr1_207752171_C_T/igv_batch_script.txt
cp work/_miniwdl_inputs/0/3599996130_r7__chr1_207752171_C_T.igv_script.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/work/_miniwdl_inputs/0/3599996130_r7__chr1_207752171_C_T.igv_script.txt
cp work/3599996130_r7__chr1_207752171_C_T/3599996130_r7__chr1_207752171_C_T_chr1_207752071_207752271.png s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/work/3599996130_r7__chr1_207752171_C_T/3599996130_r7__chr1_207752171_C_T_chr1_207752071_207752271.png
cp work/_miniwdl_inputs/0/3599996130_r7.bam.bai s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/work/_miniwdl_inputs/0/3599996130_r7.bam.bai
cp work/_miniwdl_inputs/0/3599996130_r7.bam s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/work/_miniwdl_inputs/0/3599996130_r7.bam
cp /tmp/miniwdl_task/timing.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/timing.json
cp /tmp/miniwdl_task/metrics.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/metrics.json
cp /tmp/miniwdl_task/exit_code s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/5e/5e6269c52685cb32420f3c29b12ec126/exit_code
[2026-06-02 21:03:59] [miniwdl-eks.task] Done exit_code=0 (50206ms unstage, 352600ms total)