Fixed some bugs

cae1d186 · Gonzalo S Nido · 350d3590 · cae1d186
Commit cae1d186 authored Aug 19, 2020 by Gonzalo S Nido
--- a/wgbs-pipeline.sh
+++ b/wgbs-pipeline.sh
@@ -34,12 +34,12 @@ psrecord="psrecord"
 ########################################

 # To activate CPU and RAM monitoring
-#MONITOR=false
-MONITOR=true
+MONITOR=false
+#MONITOR=true

 # To subset reads to 10,000 (debug)
-#SUBSET_READS=false
-SUBSET_READS=true
+SUBSET_READS=false
+#SUBSET_READS=true

 ########################################

@@ -161,8 +161,8 @@ if $MONITOR; then
 fi

 if $SUBSET_READS; then
-    SUBSET_READS="-u 100000"
-    echo "SUBSETTING TO 100000 READS ONLY!!!!"
+    SUBSET_READS="-u 1000000"
+    echo "SUBSETTING TO 1000000 READS ONLY!!!!"
    echo
 fi

@@ -189,7 +189,7 @@ CMD="${bismark} ${b38_ref} -1 ${R1} -2 ${R2} --multicore ${cpus} ${SUBSET_READS}
 echo -e ${CMD} > ${log_dir}/1_1_aln.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/1_1_aln.cmd" --log ${log_dir}/1_1_aln.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/1_1_aln.cmd" --log ${log_dir}/1_1_aln.resources --interval 5 --include-children
 else
    bash ${log_dir}/1_1_aln.cmd
 fi
@@ -246,7 +246,7 @@ CMD="${deduplicate_bismark} --paired --samtools_path ${samtools_path} \
 echo -e ${CMD} > ${log_dir}/1_3_dedup.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/1_3_dedup.cmd" --log ${log_dir}/1_3_dedup.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/1_3_dedup.cmd" --log ${log_dir}/1_3_dedup.resources --interval 5 --include-children
 else
    bash ${log_dir}/1_3_dedup.cmd
 fi
@@ -265,7 +265,7 @@ fi

 echo -ne "     1.4 Extracting methylation... "

-cpus=`expr ${N_proc} / 3`
+cpus=${N_proc}

 CMD="${bismark_meth_extract} -p --comprehensive --output ${output_dir} \
    --multicore ${cpus} \
@@ -276,7 +276,7 @@ CMD="${bismark_meth_extract} -p --comprehensive --output ${output_dir} \
 echo -e ${CMD} > ${log_dir}/1_4_meth.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/1_4_meth.cmd" --log ${log_dir}/1_4_meth.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/1_4_meth.cmd" --log ${log_dir}/1_4_meth.resources --interval 5 --include-children
 else
    bash ${log_dir}/1_4_meth.cmd
 fi
@@ -310,7 +310,7 @@ cat ${output_dir}/CHG_context_b38_${sample_id}.dedup.txt | python3 ${ext_chr_srt
 echo -e ${CMD} > ${log_dir}/1_5_extract_MT.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/1_5_extract_MT.cmd" --log ${log_dir}/1_5_extract_MT.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/1_5_extract_MT.cmd" --log ${log_dir}/1_5_extract_MT.resources --interval 5 --include-children
 else
    bash ${log_dir}/1_5_extract_MT.cmd
 fi
@@ -324,7 +324,6 @@ fi

 echo

-exit 1



@@ -352,7 +351,7 @@ CMD="${bismark} ${mt_ref} -1 ${R1} -2 ${R2} --multicore ${cpus} ${SUBSET_READS}
 echo -e ${CMD} > ${log_dir}/2_1_aln.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/2_1_aln.cmd" --log ${log_dir}/2_1_aln.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/2_1_aln.cmd" --log ${log_dir}/2_1_aln.resources --interval 5 --include-children
 else
    bash ${log_dir}/2_1_aln.cmd
 fi
@@ -383,7 +382,7 @@ CMD="${samtools} cat -o ${output_dir}/MT_${sample_id}.bam ${bamfile_list} > \
 echo -e ${CMD} > ${log_dir}/2_2_merge.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/2_2_merge.cmd" --log ${log_dir}/2_2_merge.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/2_2_merge.cmd" --log ${log_dir}/2_2_merge.resources --interval 5 --include-children
 else
    bash ${log_dir}/2_2_merge.cmd
 fi
@@ -402,6 +401,7 @@ fi


 echo -ne "     2.3 Dedupping alignment... "
+
 CMD="${deduplicate_bismark} --paired --samtools_path ${samtools_path} \
    --output_dir ${output_dir} ${output_dir}/MT_${sample_id}.bam > \
    ${log_dir}/2_3_dedup.stdout 2> \
@@ -409,7 +409,7 @@ CMD="${deduplicate_bismark} --paired --samtools_path ${samtools_path} \
 echo -e ${CMD} > ${log_dir}/2_3_dedup.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/2_3_dedup.cmd" --log ${log_dir}/2_3_dedup.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/2_3_dedup.cmd" --log ${log_dir}/2_3_dedup.resources --interval 5 --include-children
 else
    bash ${log_dir}/2_3_dedup.cmd
 fi
@@ -428,7 +428,7 @@ fi

 echo -ne "     2.4 Extracting methylation... "

-cpus=`expr ${N_proc} / 3`
+cpus=${N_proc}

 CMD="${bismark_meth_extract} -p --comprehensive --output ${output_dir} \
    --gzip --multicore ${cpus} \
@@ -439,7 +439,7 @@ CMD="${bismark_meth_extract} -p --comprehensive --output ${output_dir} \
 echo -e ${CMD} > ${log_dir}/2_4_meth.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/2_4_meth.cmd" --log ${log_dir}/2_4_meth.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/2_4_meth.cmd" --log ${log_dir}/2_4_meth.resources --interval 5 --include-children
 else
    bash ${log_dir}/2_4_meth.cmd
 fi
@@ -482,7 +482,7 @@ CMD="${bismark} ${nuc_ref} -1 ${R1} -2 ${R2} --multicore ${cpus} ${SUBSET_READS}
 echo -e ${CMD} > ${log_dir}/3_1_aln.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/3_1_aln.cmd" --log ${log_dir}/3_1_aln.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/3_1_aln.cmd" --log ${log_dir}/3_1_aln.resources --interval 5 --include-children
 else
    bash ${log_dir}/3_1_aln.cmd
 fi
@@ -520,7 +520,7 @@ CMD="cat ${unmapped_list_r1} > ${output_dir}/b38_noMT_${sample_id}_unmapped.R1.f
 echo -e ${CMD} > ${log_dir}/3_2_merge_unmapped.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/3_2_merge.cmd" --log ${log_dir}/3_2_merge.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/3_2_merge_unmapped.cmd" --log ${log_dir}/3_2_merge_unmapped.resources --interval 5 --include-children
 else
    bash ${log_dir}/3_2_merge_unmapped.cmd
 fi
@@ -550,7 +550,7 @@ CMD="rm ${bamfile_list}"
 echo ${CMD} > ${log_dir}/3_3_delete.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/3_3_delete.cmd" --log ${log_dir}/3_3_delete.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/3_3_delete.cmd" --log ${log_dir}/3_3_delete.resources --interval 5 --include-children
 else
    bash ${log_dir}/3_3_delete.cmd
 fi
@@ -568,21 +568,22 @@ fi
 
 echo -ne "     3.4 Re-aligning unmapped reads to mtDNA... "

-cpus=`expr ${RAM} / 16`
-if [[ $cpus -eq 0 ]]; then cpus=1; fi
+if [ "${RAM}" -lt "16" ]; then cpus=1; else cpus=$( expr ${RAM} / 16 ); fi
+echo -ne "(${cpus} cores) "

 CMD="(${bismark} ${mt_ref} -1 ${output_dir}/b38_noMT_${sample_id}_unmapped.R1.fastq.gz \
    -2 ${output_dir}/b38_noMT_${sample_id}_unmapped.R2.fastq.gz --multicore ${cpus} \
    -o ${output_dir} --prefix umap_to_MT --path_to_bowtie ${bowtie_path} \
    --samtools_path ${samtools_path} --temp_dir ${tmp_dir} && \
    mv ${output_dir}/umap_to_MT.b38_noMT_${sample_id}_unmapped.R1_bismark_bt2_pe.bam ${output_dir}/umap_to_MT_${sample_id}.bam && \
-    mv ${output_dir}/umap_to_MT.b38_noMT_${sample_id}_unmapped.R1_bismark_bt2_PE_report.txt ${output_dir}/umap_to_MT_${sample_id}_report.txt) > \
+    mv ${output_dir}/umap_to_MT.b38_noMT_${sample_id}_unmapped.R1_bismark_bt2_PE_report.txt ${output_dir}/umap_to_MT_${sample_id}_report.txt && \
+    rm ${output_dir}/b38_noMT_${sample_id}_unmapped.R?.fastq.gz) > \
    ${log_dir}/3_4_realign_to_mt.stdout 2> \
    ${log_dir}/3_4_realign_to_mt.stderr"
 echo ${CMD} > ${log_dir}/3_4_realign_to_mt.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/3_4_realign_to_mt.cmd" --log ${log_dir}/3_4_realign_to_mt.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/3_4_realign_to_mt.cmd" --log ${log_dir}/3_4_realign_to_mt.resources --interval 5 --include-children
 else
    bash ${log_dir}/3_4_realign_to_mt.cmd
 fi
@@ -595,9 +596,6 @@ else
 fi


-rm ${output_dir}/b38_noMT_${sample_id}_unmapped.R?.fastq.gz
-
-

 echo -ne "     3.5 Dedupping alignments... "

@@ -608,7 +606,7 @@ CMD="${deduplicate_bismark} --paired --samtools_path ${samtools_path} \
 echo -e ${CMD} > ${log_dir}/3_5_dedup.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/3_5_dedup.cmd" --log ${log_dir}/3_5_dedup.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/3_5_dedup.cmd" --log ${log_dir}/3_5_dedup.resources --interval 5 --include-children
 else
    bash ${log_dir}/3_5_dedup.cmd
 fi
@@ -629,7 +627,7 @@ fi

 echo -ne "     3.6 Extracting methylation in MT..."

-cpus=`expr ${N_proc} / 3`
+cpus=${N_proc}

 CMD="${bismark_meth_extract} -p --comprehensive --output ${output_dir} \
    --gzip --multicore ${cpus} \
@@ -640,7 +638,7 @@ CMD="${bismark_meth_extract} -p --comprehensive --output ${output_dir} \
 echo -e ${CMD} > ${log_dir}/3_6_meth.cmd
 if $MONITOR; then
    echo -ne "\n     "
-    ${psrecord} "bash ${log_dir}/3_6_meth.cmd" --log ${log_dir}/3_6_meth.resources --interval 60 --include-children
+    ${psrecord} "bash ${log_dir}/3_6_meth.cmd" --log ${log_dir}/3_6_meth.resources --interval 5 --include-children
 else
    bash ${log_dir}/3_6_meth.cmd
 fi