Error while FASTP is running #1347
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Can you check or post the |
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Only .command.run#!/bin/bash
# NEXTFLOW TASK: NFCORE_SAREK:SAREK:FASTP (NA12877-1)
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=$((count+1))
done
echo "%mem=${nxf_stat_ret[1]}" >> $trace_file
echo "vmem=${nxf_stat_ret[2]}" >> $trace_file
echo "rss=${nxf_stat_ret[3]}" >> $trace_file
echo "peak_vmem=${nxf_stat_ret[4]}" >> $trace_file
echo "peak_rss=${nxf_stat_ret[5]}" >> $trace_file
echo "vol_ctxt=${nxf_stat_ret[6]}" >> $trace_file
echo "inv_ctxt=${nxf_stat_ret[7]}" >> $trace_file
}
nxf_write_trace() {
echo "nextflow.trace/v2" > $trace_file
echo "realtime=$wall_time" >> $trace_file
echo "%cpu=$ucpu" >> $trace_file
echo "cpu_model=$cpu_model" >> $trace_file
echo "rchar=${io_stat1[0]}" >> $trace_file
echo "wchar=${io_stat1[1]}" >> $trace_file
echo "syscr=${io_stat1[2]}" >> $trace_file
echo "syscw=${io_stat1[3]}" >> $trace_file
echo "read_bytes=${io_stat1[4]}" >> $trace_file
echo "write_bytes=${io_stat1[5]}" >> $trace_file
}
nxf_trace_mac() {
local start_millis=$(nxf_date)
/bin/bash -euo pipefail /BiO/home/pmc09/pipeline_test/WGS_germline/00.script/work/3d/a799cee87395a369afdf75e5c9d362/.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 $mem_proc' ERR
/bin/bash -euo pipefail /BiO/home/pmc09/pipeline_test/WGS_germline/00.script/work/3d/a799cee87395a369afdf75e5c9d362/.command.sh &
local task=$!
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[*]}"
echo "nextflow.trace/v2" > $trace_file
echo "realtime=$wall_time" >> $trace_file
echo "%cpu=$ucpu" >> $trace_file
echo "cpu_model=$cpu_model" >> $trace_file
echo "rchar=${io_stat1[0]}" >> $trace_file
echo "wchar=${io_stat1[1]}" >> $trace_file
echo "syscr=${io_stat1[2]}" >> $trace_file
echo "syscw=${io_stat1[3]}" >> $trace_file
echo "read_bytes=${io_stat1[4]}" >> $trace_file
echo "write_bytes=${io_stat1[5]}" >> $trace_file
[ -e /proc/$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
}
# aws cli retry config
export AWS_RETRY_MODE=standard
export AWS_MAX_ATTEMPTS=5
# aws helper
nxf_s3_upload() {
local name=$1
local s3path=$2
if [[ "$name" == - ]]; then
aws s3 cp --only-show-errors --storage-class STANDARD - "$s3path"
elif [[ -d "$name" ]]; then
aws s3 cp --only-show-errors --recursive --storage-class STANDARD "$name" "$s3path/$name"
else
aws s3 cp --only-show-errors --storage-class STANDARD "$name" "$s3path/$name"
fi
}
nxf_s3_download() {
local source=$1
local target=$2
local file_name=$(basename $1)
local is_dir=$(aws s3 ls $source | grep -F "PRE ${file_name}/" -c)
if [[ $is_dir == 1 ]]; then
aws s3 cp --only-show-errors --recursive "$source" "$target"
else
aws s3 cp --only-show-errors "$source" "$target"
fi
}
nxf_container_env() {
cat << EOF
export PYTHONNOUSERSITE="1"
export R_PROFILE_USER="/.Rprofile"
export R_ENVIRON_USER="/.Renviron"
export JULIA_DEPOT_PATH="/usr/local/share/julia"
export PATH="\$PATH:/BiO/home/pmc09/.nextflow/assets/nf-core/sarek/bin"
EOF
}
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() {
rsync -rRl $1 $2
}
nxf_fs_rclone() {
rclone copyto $1 $2/$1
}
nxf_fs_fcp() {
fcp $1 $2/$1
}
on_exit() {
exit_status=${nxf_main_ret:=$?}
printf -- $exit_status > /BiO/home/pmc09/pipeline_test/WGS_germline/00.script/work/3d/a799cee87395a369afdf75e5c9d362/.exitcode
set +u
docker rm $NXF_BOXID &>/dev/null || true
exit $exit_status
}
on_term() {
set +e
docker stop $NXF_BOXID
}
nxf_launch() {
docker run -i --cpu-shares 12288 --memory 4096m -e "NXF_TASK_WORKDIR" -e "NXF_DEBUG=${NXF_DEBUG:=0}" -u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME -v /BiO/home/pmc09:/BiO/home/pmc09 -w "$PWD" --name $NXF_BOXID quay.io/biocontainers/fastp:0.23.4--h5f740d0_0 /bin/bash -c "eval $(nxf_container_env); /bin/bash /BiO/home/pmc09/pipeline_test/WGS_germline/00.script/work/3d/a799cee87395a369afdf75e5c9d362/.command.run nxf_trace"
}
nxf_stage() {
true
# stage input files
rm -f ERR194146_1.fastq.gz
rm -f ERR194146_2.fastq.gz
ln -s /BiO/home/pmc09/pipeline_test/WGS_germline/01.standard_samples/NA12877/ERR194146_1.fastq.gz ERR194146_1.fastq.gz
ln -s /BiO/home/pmc09/pipeline_test/WGS_germline/01.standard_samples/NA12877/ERR194146_2.fastq.gz ERR194146_2.fastq.gz
}
nxf_unstage() {
true
[[ ${nxf_main_ret:=0} != 0 ]] && return
}
nxf_main() {
trap on_exit EXIT
trap on_term TERM INT USR2
trap '' USR1
[[ "${NXF_CHDIR:-}" ]] && cd "$NXF_CHDIR"
export NXF_BOXID="nxf-$(dd bs=18 count=1 if=/dev/urandom 2>/dev/null | base64 | tr +/ 0A | tr -d '\r\n')"
NXF_SCRATCH=''
[[ $NXF_DEBUG > 0 ]] && nxf_env
touch /BiO/home/pmc09/pipeline_test/WGS_germline/00.script/work/3d/a799cee87395a369afdf75e5c9d362/.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.command.sh#!/bin/bash -euo pipefail
[ ! -f NA12877-1_1.fastq.gz ] && ln -sf ERR194146_1.fastq.gz NA12877-1_1.fastq.gz
[ ! -f NA12877-1_2.fastq.gz ] && ln -sf ERR194146_2.fastq.gz NA12877-1_2.fastq.gz
fastp \
--in1 NA12877-1_1.fastq.gz \
--in2 NA12877-1_2.fastq.gz \
--out1 NA12877-1_1.fastp.fastq.gz \
--out2 NA12877-1_2.fastp.fastq.gz \
--json NA12877-1.fastp.json \
--html NA12877-1.fastp.html \
\
\
\
--thread 12 \
--detect_adapter_for_pe \
--disable_adapter_trimming --split_by_lines 200000000 \
2> NA12877-1.fastp.log
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTP":
fastp: $(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS |
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Is this reproducible? What happens if you |
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It stops again when I resume. |
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I think I found what's wrong. I read My file may have problem. I'll check fastq file. |
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I tried with other sample (NA12878), and it works! |
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Hi,
I ran sarek for WGS data with hg19 genome, but it reports error when sarek perform FASTP.
Here is my command line and terminal output.
Command line
nextflow run nf-core/sarek \ --input /BiO/home/pmc09/pipeline_test/WGS_germline/00.script/samplesheet_1.csv \ --outdir /BiO/home/pmc09/pipeline_test/WGS_germline/02.results/NA12877/hg19 \ --genome hg19 \ --dbsnp "/BiO/Reference/dbsnp_b151_37p13.vcf.gz" \ -profile docker \ -bgTerminal output
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