P5: cloud task for cohort QC validation; configurable gp3 throughput; batched contamination map

- scripts/cloud/tasks/p5.sh: P4 preset re-check, genotype (v5) with QC, validate_p5_large.py
- scripts/validate_p5_large.py: identify samples via het pattern vs 1000G VCF; sex, parent-offspring,
  Mendel, contamination/control distributions
- trial.sh: DISK_MBPS / DISK_IOPS
- qc/contamination: bounded map batches (executor.map submits eagerly)

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

scripts/cloud/trial.sh

@@ -17,6 +17,8 @@ TYPE=${TYPE:-m7g.4xlarge}
 MAX_PRICE=${MAX_PRICE:-0.30}        # USD/hour spot cap (on-demand is 0.6528)
 MAX_MINUTES=${MAX_MINUTES:-360}     # hard cap: 6 hours
 DISK_GB=${DISK_GB:-250}
+DISK_MBPS=${DISK_MBPS:-125}         # gp3 throughput (125 = free baseline; each extra MB/s ~ $0.00005/h)
+DISK_IOPS=${DISK_IOPS:-3000}        # gp3 IOPS (3000 = free baseline)
 BUDGET_USD=${BUDGET_USD:-10}
 TASK=${TASK:-p3}                 # scripts/cloud/tasks/<TASK>.sh
 TAG=simurg-trial
@@ -72,7 +74,7 @@ launch)
     --iam-instance-profile Name=$ROLE \
     --instance-initiated-shutdown-behavior terminate \
     --instance-market-options "MarketType=spot,SpotOptions={MaxPrice=$MAX_PRICE,SpotInstanceType=one-time,InstanceInterruptionBehavior=terminate}" \
-    --block-device-mappings "DeviceName=/dev/sda1,Ebs={VolumeSize=$DISK_GB,VolumeType=gp3,DeleteOnTermination=true}" \
+    --block-device-mappings "DeviceName=/dev/sda1,Ebs={VolumeSize=$DISK_GB,VolumeType=gp3,Throughput=$DISK_MBPS,Iops=$DISK_IOPS,DeleteOnTermination=true}" \
     --metadata-options HttpTokens=required \
     --user-data file:///tmp/simurg-userdata.sh \
     --tag-specifications "ResourceType=instance,Tags=[{Key=Project,Value=$TAG},{Key=Run,Value=$RUN}]" \