Replica node failure due to script execution

Greetings, we need assistance in determining the cause of our issue with Mongo cluster.

Cluster settings:

• 3 nodes

• Run on VMware vCenter VMs

• MongoDB shell version v4.2.2

Static hostname: m1-prod-vm-db-mongo02
Icon name: computer-vm
Chassis: vm
Machine ID: 8edfb1744b9947f4a12093a8259d93d0
Boot ID: aed3637a32ca449798827711859ac700
Virtualization: vmware
Operating System: Red Hat Enterprise Linux Server 7.6 (Maipo)
CPE OS Name: cpe:/o:redhat:enterprise_linux:7.6:GA:server
Kernel: Linux 3.10.0-957.27.2.el7.x86_64
Architecture: x86-64

During the execution of the script which updates the data in collections we encountered a failure of one of replica nodes. (update.txt)

To repair the cluster we performed the following:

1. Changed the /etc/mongod.conf on failed node - switched the port to 27108 and commented replication settings to run in standalone mode.

1. Executed the same script on the failed node in standalone mode, it finished successfully 

1. Synced the collections with data from healthy replica node using the script :

   #!/bin/bash

   BEGIN_DATE=$1

   LAST_DATE=$2

   LOCAL_DATABASE=audit_prod

   REMOTE_DATABASE=audit_prod

   REMOTE_HOST=m1-prod-vm-db-mongo02

   CURRENT_DATE=$BEGIN_DATE

   while [$CURRENT_DATE!= $LAST_DATE];

   do echo "Текущая дата: $CURRENT_DATE"

   mongodump --db="${LOCAL_DATABASE}" --collection="${CURRENT_DATE}" --archive | ssh "${REMOTE_HOST}" -T "mongorestore --archive --port=27018"

   echo "Дата завершения сбора синхронизации: $CURRENT_DATE"

   CURRENT_DATE=$(date -d "${CURRENT_DATE} +1 день" +%F) Готово

1. Synced the oplog collection from healthy replica to the failed one

   mongodump -d local -c oplog.rs -o /data/dump/oplog

   scp -rp /data/dump/ <username>@<hostname>:/data/dump/

   mongorestore -vvvv -d local --port=27018 / вывод данных/

1. Restored the initial config on failed node.

The logs during the failure (logs.txt)