previous fixes

src/analysis/persephone/SeqC_pipeline/BASH_seqc_mama.sh

@@ -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
@@ -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
@@ -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[@]}
@@ -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 ${vt_R} ]];then
@@ -1724,12 +1728,21 @@ for istep in "${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}','${venv_mem_max}' }'
 		fi
 		#WORKING EX
@@ -1986,7 +1999,7 @@ for istep in "${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 ${v_kjoin_out/out/mpa_out} -n 1 ) )
@@ -2006,7 +2019,7 @@ for istep in "${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