miniwdl.log - Workdir - call-igv_snapshot-13/call-igv_snapshot

File Info

Filename: miniwdl.log
Full Path: s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/miniwdl.log
Size: 6.0 KB
Task: call-igv_snapshot-13/call-igv_snapshot
Attempt
Content

[2026-06-02 20:57:35] [miniwdl-eks.task] Staging: downloading command and 3 inputs
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/command /tmp/miniwdl_task/command
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/23/2394aa529a0ed9ebc9919045e3b57b58/work/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G.igv_script.txt /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G.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/3574260338_r7.bam.bai /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_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/3574260338_r7.bam /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam
[2026-06-02 20:58:11] [miniwdl-eks.task] Staging completed (3 inputs, 35131ms) s5cmd=workers:256,concurrency:10,cpus:24
+ BAM_TOKEN=/tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam
+ INDEX_TOKEN=/tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam.bai
+ mkdir 3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G
+ sed 's|::BAM_FILE::|/tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam index=/tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam.bai|g' /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G.igv_script.txt
+ XVFB_PID=109
+ DISPLAY=:13
+ /igv/jdk-11/bin/java --module-path=/igv/lib -Xmx5g @/igv/igv.args --module=org.igv/org.broad.igv.ui.Main -b 3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G/igv_batch_script.txt
+ Xvfb :13
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 8:58:11 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: 3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G/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 21:02] [TrackLoader] Loading resource:  /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam
WARNING: BAM index file /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam.bai is older than BAM /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam
WARNING: BAM index file /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam.bai is older than BAM /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam
WARNING: BAM index file /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam.bai is older than BAM /tmp/miniwdl_task/work/_miniwdl_inputs/0/3574260338_r7.bam
INFO [Jun 02,2026 21:02] [ShutdownThread] Shutting down
+ kill 109
[2026-06-02 21:02:58] [miniwdl-eks.task] Task finished exit_code=0 (287866ms)
cp /tmp/miniwdl_task/stdout.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/stdout.txt
cp /tmp/miniwdl_task/stderr.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/stderr.txt
cp work/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G/igv_batch_script.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/work/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G/igv_batch_script.txt
cp work/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G_chr1_207767560_207767760.png s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/work/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G_chr1_207767560_207767760.png
cp work/_miniwdl_inputs/0/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G.igv_script.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/work/_miniwdl_inputs/0/3574260338_r7__chr1_207767660_GCTTCTTCCTTATATGT_G.igv_script.txt
cp work/_miniwdl_inputs/0/3574260338_r7.bam.bai s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/work/_miniwdl_inputs/0/3574260338_r7.bam.bai
cp work/_miniwdl_inputs/0/3574260338_r7.bam s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/work/_miniwdl_inputs/0/3574260338_r7.bam
cp /tmp/miniwdl_task/timing.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/timing.json
cp /tmp/miniwdl_task/metrics.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/metrics.json
cp /tmp/miniwdl_task/exit_code s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/fc/fc81e7034263f3e40a7946cb36a4006f/exit_code
[2026-06-02 21:03:46] [miniwdl-eks.task] Done exit_code=0 (47344ms unstage, 370343ms total)