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Hotfix for seqc_mama primary bash script #2448

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Hotfix for seqc_mama primary bash script #2448

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27 changes: 20 additions & 7 deletions src/analysis/persephone/SeqC_pipeline/BASH_seqc_mama.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# Title: mama script: take run commands, est db link, run stepgen
# Program by: Wiley Barton - 2022.02.27
# Modified for conda/docker pipeline - 2024.02.22
# last update - 2025.01.30
# last update - 2025.02.25
# Modified code sources:
# https://stackoverflow.com/questions/2043453/executing-multi-line-statements-in-the-one-line-command-line
# Notes: generate bash files according to user input for the completion of pipeline
Expand Down Expand Up @@ -36,6 +36,7 @@
# flesh out func_demo to build complete demo run within /DB/DEPO_demo
# auto compile file list from input dir in absence of provided list
# expand splash to include system params: cpu, mem, du of key directories
# implement pv for progress bar... tar -I pigz -xvf stuff.tar.gz | pv
#refs
# prodigal:https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-119#citeas
# https://www.cyberciti.biz/tips/bash-shell-parameter-substitution-2.html
Expand All @@ -53,6 +54,8 @@ var_rep_len=${#var_rep_ary[@]}
#size check -db
v_vol_real=$(du -bs $v_dir_db | cut -f1 )
v_vol_none=60000
#system max cpu
v_sys_mem=$(nproc)
v_scrp_check=0
#var_rep_ary[var_rep_len]='x/y/z/cat'*'.kitty'
#var_rep_out=${var_rep_ary[@]}
Expand Down Expand Up @@ -1518,6 +1521,7 @@ if (( ${vopt_log} ));then
fi
printf 'Input file type: %s\n%s\n' "${vopt_file_type}" "${v_logblock1}" >> ${v_logfile}
# Check zip status - CRIT - extend to .tar files in dir
# pot. just exclude .tar
vt_L=$( printf '%s\n' "${v_file_in_good[@]}" | grep -E "\.gz|gzip$" | wc -l )
vt_R='0'
if [[ ${vt_L} -gt ${vt_R} ]];then
Expand Down Expand Up @@ -1724,12 +1728,21 @@ for istep in "${vopt_step[@]}";do
vin_head=''
vin_tail=''
fi
# proc check - ensure that too many processes are not called
if [[ -z ${venv_proc_max} ]];then
venv_proc_max=$(( ${venv_cpu_max} / 2 ))
fi
if [[ $(printf %.0f $(echo "${venv_cpu_max} * ${venv_proc_max}" | bc -l)) -gt "${v_sys_mem}" ]];then
vt="${venv_proc_max}"
while [[ $(printf %.0f $(echo "${venv_cpu_max} * ${vt}" | bc -l)) -gt "${v_sys_mem}" ]];do
((vt--))
#printf 'in%s\n' "${vt}"
done
#printf 'out%s\n' "${vt}"
venv_proc_max="${vt}"
fi
if [[ ${vopt_com_log} -eq 0 ]];then
#insert as awk print block - ex: vopt_com='{ printf "--output-format tsv --output-basename %s",va_nID }'
#improve with adjustment to :--processes <1>
if [[ -z ${venv_proc_max} ]];then
venv_proc_max=$(( ${venv_cpu_max} / 2 ))
fi
vin_com='{ printf " --remove-intermediate-output --reference-db %s --threads %s --processes %s --max-memory %sg --trimmomatic /opt/conda/envs/env_s1_kneaddata/share/trimmomatic --reorder","'${vin_host_rm}'",'${venv_cpu_max}','${venv_proc_max}','${venv_mem_max}' }'
fi
#WORKING EX
Expand Down Expand Up @@ -1986,7 +1999,7 @@ for istep in "${vopt_step[@]}";do
v_k2mpa_out=${v_kjoin_out/out/mpa_out_RA}
cat ${v_kjoin_out/out/mpa_out} | cut --fields 2${v_bk_col_frac} > "${v_k2mpa_out}"
#drop col type for match with meta data
sed -i "1 s/_$v_match//" "${v_k2mpa_out}"
sed -i "1,1s/_$v_match//g" "${v_k2mpa_out}"
#counts
v_match='num'
v_bk_cols=( $( head ${v_kjoin_out/out/mpa_out} -n 1 ) )
Expand All @@ -2006,7 +2019,7 @@ for istep in "${vopt_step[@]}";do
v_k2mpa_out=${v_kjoin_out/out/mpa_out_RC}
cat ${v_kjoin_out/out/mpa_out} | cut --fields 2${v_bk_col_num} > "${v_k2mpa_out}"
#drop col type for match with meta data
sed -i "1 s/_$v_match//" "${v_k2mpa_out}"
sed -i "1,1s/_$v_match//g" "${v_k2mpa_out}"
#default mars input is now "${v_k2mpa_out}" = /DB/DEPO_proc/step2_kraken/KB_S_mpa_out_RC.txt
vout_sX=${vout_s2}
# step keep-clean
Expand Down