Hi,
I have been using Seqera platform for many years now and for some reason, a few weeks ago, all my previous pipeline that use to complete successfully now all errors with the same bash error from the .command.run script. Some variables (end_millis and|or start_millis). This as been really impacting my ability to work and if someone can help here, I’d be so so releived!
This is a very basic nextflow script I am using that error on Seqera Platform (but fully work when run locally). It can be found on git hub as nf-seqera-test
workflow {
def ch_fastq_files = channel.fromPath("s3://liftoff-seqera-work/test_data/test.txt")
CAT_FILES(ch_fastq_files)
}
process CAT_FILES {
container "ubuntu"
input:
path files
output:
path "merged.txt"
script:
"""
cat ${files} ${files} > merged.txt
"""
}
And this the error I am geting:
The exit status of the task that caused the workflow execution to fail was: 1
The failure reason of the task that caused the workflow execution to fail was: .command.run: line 178: Unexpected: unbound variable
Error executing process > 'CAT_FILES (1)'
Caused by:
Essential container in task exited
Command executed:
cat test.txt test.txt > merged.txt
Command exit status:
1
Command output:
(empty)
Command error:
.command.run: line 178: Unexpected: unbound variable
Work dir:
s3://liftoff-seqera-work/scratch/2WrrFu9JFJeYAA/b2/3b2fa8f1ce1fdeb94901e514d4ce0f
Container:
ubuntu
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
The error originates from the .command.run bash srcript:
#!/bin/bash
### ---
### name: 'CAT_FILES (1)'
### container: 'ubuntu'
### outputs:
### - 'merged.txt'
### ...
set -e
set -u
NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
NXF_ENTRY=${1:-nxf_main}
nxf_tree() {
local pid=$1
declare -a ALL_CHILDREN
while read P PP;do
ALL_CHILDREN[$PP]+=" $P"
done < <(ps -e -o pid= -o ppid=)
pstat() {
local x_pid=$1
local STATUS=$(2> /dev/null < /proc/$1/status grep -E 'Vm|ctxt')
if [ $? = 0 ]; then
local x_vsz=$(echo "$STATUS" | grep VmSize | awk '{print $2}' || echo -n '0')
local x_rss=$(echo "$STATUS" | grep VmRSS | awk '{print $2}' || echo -n '0')
local x_peak=$(echo "$STATUS" | grep -E 'VmPeak|VmHWM' | sed 's/^.*:\s*//' | sed 's/[\sa-zA-Z]*$//' | tr '\n' ' ' || echo -n '0 0')
local x_pmem=$(awk -v rss=$x_rss -v mem_tot=$mem_tot 'BEGIN {printf "%.0f", rss/mem_tot*100*10}' || echo -n '0')
local vol_ctxt=$(echo "$STATUS" | grep '\bvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
local inv_ctxt=$(echo "$STATUS" | grep '\bnonvoluntary_ctxt_switches' | awk '{print $2}' || echo -n '0')
cpu_stat[x_pid]="$x_pid $x_pmem $x_vsz $x_rss $x_peak $vol_ctxt $inv_ctxt"
fi
}
pwalk() {
pstat $1
for i in ${ALL_CHILDREN[$1]:=}; do pwalk $i; done
}
pwalk $1
}
nxf_stat() {
cpu_stat=()
nxf_tree $1
declare -a sum=(0 0 0 0 0 0 0 0)
local pid
local i
for pid in "${!cpu_stat[@]}"; do
local row=(${cpu_stat[pid]})
[ $NXF_DEBUG = 1 ] && echo "++ stat mem=${row[*]}"
for i in "${!row[@]}"; do
if [ $i != 0 ]; then
sum[i]=$((sum[i]+row[i]))
fi
done
done
[ $NXF_DEBUG = 1 ] && echo -e "++ stat SUM=${sum[*]}"
for i in {1..7}; do
if [ ${sum[i]} -lt ${cpu_peak[i]} ]; then
sum[i]=${cpu_peak[i]}
else
cpu_peak[i]=${sum[i]}
fi
done
[ $NXF_DEBUG = 1 ] && echo -e "++ stat PEAK=${sum[*]}\n"
nxf_stat_ret=(${sum[*]})
}
nxf_mem_watch() {
set -o pipefail
local pid=$1
local trace_file=.command.trace
local count=0;
declare -a cpu_stat=(0 0 0 0 0 0 0 0)
declare -a cpu_peak=(0 0 0 0 0 0 0 0)
local mem_tot=$(< /proc/meminfo grep MemTotal | awk '{print $2}')
local timeout
local DONE
local STOP=''
[ $NXF_DEBUG = 1 ] && nxf_sleep 0.2 && ps fx
while true; do
nxf_stat $pid
if [ $count -lt 10 ]; then timeout=1;
elif [ $count -lt 120 ]; then timeout=5;
else timeout=30;
fi
read -t $timeout -r DONE || true
[[ $DONE ]] && break
if [ ! -e /proc/$pid ]; then
[ ! $STOP ] && STOP=$(nxf_date)
[ $(($(nxf_date)-STOP)) -gt 10000 ] && break
fi
count=$((count+1))
done
printf "%s\n" \
"%mem=${nxf_stat_ret[1]}" \
"vmem=${nxf_stat_ret[2]}" \
"rss=${nxf_stat_ret[3]}" \
"peak_vmem=${nxf_stat_ret[4]}" \
"peak_rss=${nxf_stat_ret[5]}" \
"vol_ctxt=${nxf_stat_ret[6]}" \
"inv_ctxt=${nxf_stat_ret[7]}" >> "$trace_file" || >&2 echo "Error: Failed to append to file: $trace_file"
}
nxf_write_trace() {
printf "%s\n" \
"nextflow.trace/v2" \
"realtime=$wall_time" \
"%cpu=$ucpu" \
"cpu_model=$cpu_model" \
"rchar=${io_stat1[0]}" \
"wchar=${io_stat1[1]}" \
"syscr=${io_stat1[2]}" \
"syscw=${io_stat1[3]}" \
"read_bytes=${io_stat1[4]}" \
"write_bytes=${io_stat1[5]}" >| "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
}
nxf_trace_mac() {
local start_millis=$(nxf_date)
/bin/bash -ue .command.sh
local end_millis=$(nxf_date)
local wall_time=$((end_millis-start_millis))
local ucpu=''
local cpu_model=''
local io_stat1=('' '' '' '' '' '')
nxf_write_trace
}
nxf_fd() {
local FD=11
while [ -e /proc/$$/fd/$FD ]; do FD=$((FD+1)); done
echo $FD
}
nxf_trace_linux() {
local pid=$$
command -v ps &>/dev/null || { >&2 echo "Command 'ps' required by nextflow to collect task metrics cannot be found"; exit 1; }
local num_cpus=$(< /proc/cpuinfo grep '^processor' -c)
local cpu_model=$(< /proc/cpuinfo grep '^model name' | head -n 1 | awk 'BEGIN{FS="\t: "} { print $2 }')
local tot_time0=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
local cpu_time0=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
local io_stat0=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
local start_millis=$(nxf_date)
trap 'kill $mem_proc' ERR
/bin/bash -ue .command.sh &
local task=$!
mem_fd=$(nxf_fd)
eval "exec $mem_fd> >(nxf_mem_watch $task)"
local mem_proc=$!
wait $task
local end_millis=$(nxf_date)
local tot_time1=$(grep '^cpu ' /proc/stat | awk '{sum=$2+$3+$4+$5+$6+$7+$8+$9; printf "%.0f",sum}')
local cpu_time1=$(2> /dev/null < /proc/$pid/stat awk '{printf "%.0f", ($16+$17)*10 }' || echo -n 'X')
local ucpu=$(awk -v p1=$cpu_time1 -v p0=$cpu_time0 -v t1=$tot_time1 -v t0=$tot_time0 -v n=$num_cpus 'BEGIN { pct=(p1-p0)/(t1-t0)*100*n; printf("%.0f", pct>0 ? pct : 0) }' )
local io_stat1=($(2> /dev/null < /proc/$pid/io sed 's/^.*:\s*//' | head -n 6 | tr '\n' ' ' || echo -n '0 0 0 0 0 0'))
local i
for i in {0..5}; do
io_stat1[i]=$((io_stat1[i]-io_stat0[i]))
done
local wall_time=$((end_millis-start_millis))
[ $NXF_DEBUG = 1 ] && echo "+++ STATS %CPU=$ucpu TIME=$wall_time I/O=${io_stat1[*]}"
printf "%s\n" \
"nextflow.trace/v2" \
"realtime=$wall_time" \
"%cpu=$ucpu" \
"cpu_model=$cpu_model" \
"rchar=${io_stat1[0]}" \
"wchar=${io_stat1[1]}" \
"syscr=${io_stat1[2]}" \
"syscw=${io_stat1[3]}" \
"read_bytes=${io_stat1[4]}" \
"write_bytes=${io_stat1[5]}" >| "$trace_file" || >&2 echo "Error: Failed to write to file: $trace_file"
[ -e /proc/$mem_proc ] && eval "echo 'DONE' >&$mem_fd" || true
wait $mem_proc 2>/dev/null || true
while [ -e /proc/$mem_proc ]; do nxf_sleep 0.1; done
}
nxf_trace() {
local trace_file=.command.trace
touch $trace_file
if [[ $(uname) = Darwin ]]; then
nxf_trace_mac
else
nxf_trace_linux
fi
}
# bash helper functions
nxf_cp_retry() {
local max_attempts=10
local timeout=10
local attempt=0
local exitCode=0
while (( $attempt < $max_attempts ))
do
if "$@"
then
return 0
else
exitCode=$?
fi
if [[ $exitCode == 0 ]]
then
break
fi
nxf_sleep $timeout
attempt=$(( attempt + 1 ))
timeout=$(( timeout * 2 ))
done
}
nxf_parallel() {
IFS=$'\n'
local cmd=("$@")
local cpus=$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
local max=$(if (( cpus>4 )); then echo 4; else echo $cpus; fi)
local i=0
local pid=()
(
set +u
while ((i<${#cmd[@]})); do
local copy=()
for x in "${pid[@]}"; do
# if the process exist, keep in the 'copy' array, otherwise wait on it to capture the exit code
# see https://github.com/nextflow-io/nextflow/pull/4050
[[ -e /proc/$x ]] && copy+=($x) || wait $x
done
pid=("${copy[@]}")
if ((${#pid[@]}>=$max)); then
nxf_sleep 0.2
else
eval "${cmd[$i]}" &
pid+=($!)
((i+=1))
fi
done
for p in "${pid[@]}"; do
wait $p
done
)
unset IFS
}
# aws cli retry config
export AWS_RETRY_MODE=standard
export AWS_MAX_ATTEMPTS=10
# aws helper
nxf_s3_upload() {
local name=$1
local s3path=$2
if [[ "$name" == - ]]; then
/home/ec2-user/miniconda/bin/aws --region us-east-1 s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
elif [[ -d "$name" ]]; then
/home/ec2-user/miniconda/bin/aws --region us-east-1 s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
else
/home/ec2-user/miniconda/bin/aws --region us-east-1 s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
fi
}
nxf_s3_download() {
local source=$1
local target=$2
local file_name=$(basename $1)
local is_dir=$(/home/ec2-user/miniconda/bin/aws --region us-east-1 s3 ls $source | grep -F "PRE ${file_name}/" -c)
if [[ $is_dir == 1 ]]; then
/home/ec2-user/miniconda/bin/aws --region us-east-1 s3 cp --only-show-errors --recursive "$source" "$target"
else
/home/ec2-user/miniconda/bin/aws --region us-east-1 s3 cp --only-show-errors "$source" "$target"
fi
}
nxf_sleep() {
sleep $1 2>/dev/null || sleep 1;
}
nxf_date() {
local ts=$(date +%s%3N);
if [[ ${#ts} == 10 ]]; then echo ${ts}000
elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
elif [[ ${#ts} == 13 ]]; then echo $ts
else echo "Unexpected timestamp value: $ts"; exit 1
fi
}
nxf_env() {
echo '============= task environment ============='
env | sort | sed "s/\(.*\)AWS\(.*\)=\(.\{6\}\).*/\1AWS\2=\3xxxxxxxxxxxxx/"
echo '============= task output =================='
}
nxf_kill() {
declare -a children
while read P PP;do
children[$PP]+=" $P"
done < <(ps -e -o pid= -o ppid=)
kill_all() {
[[ $1 != $$ ]] && kill $1 2>/dev/null || true
for i in ${children[$1]:=}; do kill_all $i; done
}
kill_all $1
}
nxf_mktemp() {
local base=${1:-/tmp}
mkdir -p "$base"
if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX
else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX
fi
}
nxf_fs_copy() {
local source=$1
local target=$2
local basedir=$(dirname $1)
mkdir -p $target/$basedir
cp -fRL $source $target/$basedir
}
nxf_fs_move() {
local source=$1
local target=$2
local basedir=$(dirname $1)
mkdir -p $target/$basedir
mv -f $source $target/$basedir
}
nxf_fs_rsync() {
local source=$1
local target=$2
mkdir -p $target
rsync -rRl $source $target
}
nxf_fs_rclone() {
rclone copyto $1 $2/$1
}
nxf_fs_fcp() {
fcp $1 $2/$1
}
on_exit() {
local last_err=$?
local exit_status=${nxf_main_ret:=0}
[[ ${exit_status} -eq 0 && ${nxf_unstage_ret:=0} -ne 0 ]] && exit_status=${nxf_unstage_ret:=0}
[[ ${exit_status} -eq 0 && ${last_err} -ne 0 ]] && exit_status=${last_err}
printf -- $exit_status | nxf_s3_upload - s3://liftoff-seqera-work/scratch/4h2hxIVLACw3ys/5a/f06ef60988de1569fb03f4113826ce/.exitcode || true
set +u
rm -rf $NXF_SCRATCH || true
exit $exit_status
}
on_term() {
set +e
[[ "$pid" ]] && nxf_kill $pid
}
nxf_launch() {
/bin/bash .command.run nxf_trace
}
nxf_stage() {
true
# stage input files
downloads=(true)
rm -f test.txt
rm -f .command.sh
rm -f .command.run
downloads+=("nxf_s3_download s3://liftoff-seqera-work/test_data/test.txt test.txt")
downloads+=("nxf_s3_download s3://liftoff-seqera-work/scratch/4h2hxIVLACw3ys/5a/f06ef60988de1569fb03f4113826ce/.command.sh .command.sh")
downloads+=("nxf_s3_download s3://liftoff-seqera-work/scratch/4h2hxIVLACw3ys/5a/f06ef60988de1569fb03f4113826ce/.command.run .command.run")
nxf_parallel "${downloads[@]}"
}
nxf_unstage_outputs() {
true
uploads=()
IFS=$'\n'
for name in $(eval "ls -1d merged.txt" | sort | uniq); do
uploads+=("nxf_s3_upload '$name' s3://liftoff-seqera-work/scratch/4h2hxIVLACw3ys/5a/f06ef60988de1569fb03f4113826ce")
done
unset IFS
nxf_parallel "${uploads[@]}"
}
nxf_unstage_controls() {
true
nxf_s3_upload .command.out s3://liftoff-seqera-work/scratch/4h2hxIVLACw3ys/5a/f06ef60988de1569fb03f4113826ce || true
nxf_s3_upload .command.err s3://liftoff-seqera-work/scratch/4h2hxIVLACw3ys/5a/f06ef60988de1569fb03f4113826ce || true
nxf_s3_upload .command.trace s3://liftoff-seqera-work/scratch/4h2hxIVLACw3ys/5a/f06ef60988de1569fb03f4113826ce || true
}
nxf_unstage() {
if [[ ${nxf_main_ret:=0} == 0 ]]; then
(set -e -o pipefail; (nxf_unstage_outputs | tee -a .command.out) 3>&1 1>&2 2>&3 | tee -a .command.err)
nxf_unstage_ret=$?
fi
nxf_unstage_controls
}
nxf_main() {
trap on_exit EXIT
trap on_term TERM INT USR2
trap '' USR1
[[ "${NXF_CHDIR:-}" ]] && cd "$NXF_CHDIR"
NXF_SCRATCH="$(set +u; nxf_mktemp $TMPDIR)"
[[ $NXF_DEBUG > 0 ]] && nxf_env
echo start | nxf_s3_upload - s3://liftoff-seqera-work/scratch/4h2hxIVLACw3ys/5a/f06ef60988de1569fb03f4113826ce/.command.begin
set +u
set -u
[[ $NXF_SCRATCH ]] && cd $NXF_SCRATCH
export NXF_TASK_WORKDIR="$PWD"
nxf_stage
set +e
(set -o pipefail; (nxf_launch | tee .command.out) 3>&1 1>&2 2>&3 | tee .command.err) &
pid=$!
wait $pid || nxf_main_ret=$?
nxf_unstage
}
$NXF_ENTRY
And this was run on Seqera Platform using the most basic CE:
```
{
"computeEnv": {
"id": "5z35NkSKFSR8XIDIYbZxO",
"name": "ce_basic",
"description": null,
"platform": "aws-batch",
"config": {
"workDir": "s3://liftoff-seqera-work",
"preRunScript": null,
"postRunScript": null,
"environment": [],
"nextflowConfig": null,
"region": "us-east-1",
"computeQueue": "TowerForge-5z35NkSKFSR8XIDIYbZxO-work",
"dragenQueue": null,
"dragenInstanceType": null,
"computeJobRole": null,
"executionRole": "arn:aws:iam::XXXXXXXXXXXX:role/TowerForge-5z35NkSKFSR8XIDIYbZxO-ExecutionRole",
"headQueue": "TowerForge-5z35NkSKFSR8XIDIYbZxO-head",
"headJobRole": null,
"cliPath": "/home/ec2-user/miniconda/bin/aws",
"volumes": [],
"headJobCpus": null,
"headJobMemoryMb": null,
"waveEnabled": false,
"fusion2Enabled": false,
"nvnmeStorageEnabled": false,
"logGroup": null,
"fusionSnapshots": false,
"forge": {
"type": "SPOT",
"minCpus": 0,
"maxCpus": 2500,
"gpuEnabled": false,
"ebsAutoScale": null,
"instanceTypes": [],
"allocStrategy": null,
"imageId": null,
"vpcId": null,
"subnets": [],
"securityGroups": [],
"fsxMount": null,
"fsxName": null,
"fsxSize": null,
"disposeOnDeletion": true,
"ec2KeyPair": null,
"allowBuckets": [],
"ebsBlockSize": null,
"fusionEnabled": null,
"bidPercentage": null,
"efsCreate": false,
"efsId": null,
"efsMount": null,
"dragenEnabled": false,
"dragenAmiId": null,
"ebsBootSize": null,
"ecsConfig": null,
"fargateHeadEnabled": null,
"arm64Enabled": null,
"dragenInstanceType": null
},
"forgedResources": [
{
"IamRole": "arn:aws:iam::XXXXXXXXXXXX:role/TowerForge-5z35NkSKFSR8XIDIYbZxO-ServiceRole"
},
{
"IamRole": "arn:aws:iam::XXXXXXXXXXXX:role/TowerForge-5z35NkSKFSR8XIDIYbZxO-ExecutionRole"
},
{
"IamInstanceProfile": "arn:aws:iam::XXXXXXXXXXXX:instance-profile/TowerForge-5z35NkSKFSR8XIDIYbZxO-InstanceRole"
},
{
"Ec2LaunchTemplate": "TowerForge-5z35NkSKFSR8XIDIYbZxO"
},
{
"BatchEnv": "arn:aws:batch:us-east-1:XXXXXXXXXXXX:compute-environment/TowerForge-5z35NkSKFSR8XIDIYbZxO-head"
},
{
"BatchQueue": "arn:aws:batch:us-east-1:XXXXXXXXXXXX:job-queue/TowerForge-5z35NkSKFSR8XIDIYbZxO-head"
},
{
"BatchEnv": "arn:aws:batch:us-east-1:XXXXXXXXXXXX:compute-environment/TowerForge-5z35NkSKFSR8XIDIYbZxO-work"
},
{
"BatchQueue": "arn:aws:batch:us-east-1:XXXXXXXXXXXX:job-queue/TowerForge-5z35NkSKFSR8XIDIYbZxO-work"
}
],
"deletedResources": [],
"discriminator": "aws-batch"
},
"dateCreated": "2026-06-03T17:50:03Z",
"lastUpdated": "2026-06-03T17:50:50Z",
"lastUsed": "2026-06-03T18:27:04Z",
"deleted": null,
"status": "AVAILABLE",
"message": null,
"primary": null,
"credentialsId": "XXXXXXXXXXXX",
"managedIdentityId": null,
"orgId": null,
"workspaceId": null,
"labels": null,
"resources": null,
"awsAccountId": null
}
}
And for full completeness, here’s the Nextflow log
nf-2NzJWqyiitCIgs.log (66.2 KB)
Many many thanks in advance.
Marco