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)

scripts/cloud/tasks/p5.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+# Phase P5 bundle on the 1000 Genomes Omni2.5 set (2141 samples):
+#   1. P4 re-check with --preset autocall-1.6.2 (expect byte-identical GTCs except the K-009 samples);
+#   2. `simurg genotype` (legacy preset, GTC v5 so BAF exists) with control tables and cohort QC;
+#   3. P5 validation against the 1000G pedigree and VCF (scripts/validate_p5_large.py).
+# Args: <data dir with bpm/egt and data/>  <results dir>
+set -uo pipefail
+D=$1; OUT=$2
+SRC=s3://1000genomes/release/20130502/supporting/hd_genotype_chip
+mkdir -p $OUT/p4 $OUT/p5 $D/egt
+cp $D/HumanOmni2.5-4v1-Multi_B.egt $D/egt/
+
+echo "=== P4 preset re-check $(date -u +%T) ==="
+/usr/bin/time -v .venv/bin/python scripts/validate_p4_large.py --root $D/data --bpm $D/HumanOmni2.5-4v1-Multi_B.bpm \
+  --egt-dir $D/egt --out $OUT/p4/summary.json --workers "$(nproc)" 2> $OUT/p4/time.txt \
+  || echo "P4 validation reported differences"
+tail -22 $OUT/p4/time.txt
+
+echo "=== P5 genotype + QC $(date -u +%T) ==="
+GT=/work/gt
+/usr/bin/time -v .venv/bin/simurg genotype --bpm $D/HumanOmni2.5-4v1-Multi_B.bpm --egt $D/HumanOmni2.5-4v1-Multi_B.egt \
+  --idats $D/data --out $GT --preset autocall-1.6.2 --gtc-version 5 --autocall-date "1/1/2026 12:00:00 AM" \
+  --qc-profile genotyping --threads "$(nproc)" --quiet 2> $OUT/p5/genotype_time.txt || echo "genotype exit $?"
+tail -22 $OUT/p5/genotype_time.txt
+cp $GT/sample_summary.tsv $GT/controls_qc.tsv $GT/relatedness.tsv $GT/run_manifest.json $OUT/p5/ 2>/dev/null
+cp $GT/mendel.tsv $OUT/p5/ 2>/dev/null
+cp -r $GT/logs $OUT/p5/ 2>/dev/null
+gzip -c $GT/controls_raw.tsv > $OUT/p5/controls_raw.tsv.gz 2>/dev/null
+df -h /work | tail -1
+
+echo "=== P5 validation $(date -u +%T) ==="
+aws s3 cp --no-sign-request "$SRC/broad_intensities/Omni25_genotypes_2141_samples.b37.v2.vcf.gz" /work/ --only-show-errors
+aws s3 cp --no-sign-request "s3://1000genomes/release/20130502/integrated_call_samples.20130502.ALL.ped" /work/ --only-show-errors
+/usr/bin/time -v .venv/bin/python scripts/validate_p5_large.py --gt-dir $GT --bpm $D/HumanOmni2.5-4v1-Multi_B.bpm \
+  --vcf /work/Omni25_genotypes_2141_samples.b37.v2.vcf.gz --ped /work/integrated_call_samples.20130502.ALL.ped \
+  --out $OUT/p5/summary.json --workers "$(nproc)" 2> $OUT/p5/validate_time.txt || echo "P5 validation reported differences"
+tail -22 $OUT/p5/validate_time.txt
+echo "=== task done $(date -u +%T) ==="

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}]" \