test/cmdlinetest-nohmmratac

   1 #!/bin/bash
   2 # Time-stamp: <2022-06-06 12:13:43 Tao Liu>
   3
   4 # integrative subcmds testing
   5
   6 if [ $# -lt 1 ];then
   7     echo "Run all tests for subcommands of MACS3. Need >=1 parameter for a tag name! A unique string combining date, time and MACS3 version is recommended. ./test.sh <TAG> [UPDATE]\n If UPDATE is set with anything, aka, this command sees a second parameter, the standard output results will be replaced."
   8     exit
   9 fi
  10
  11 TAG=$1
  12 if [ "$#" = "2" ];then
  13     REPLACE="Y"
  14 else
  15     REPLACE="N"
  16 fi
  17
  18 TEMPDIR=../temp
  19 OUTPUTDIR_PREFIX=${TEMPDIR}/${TAG}
  20
  21 # make temp directory if necessary
  22 if [ ! -d $TEMPDIR ]; then mkdir $TEMPDIR; fi
  23
  24 CHIP=CTCF_SE_ChIP_chr22_50k.bed.gz
  25 CTRL=CTCF_SE_CTRL_chr22_50k.bed.gz
  26
  27 CHIPPE=CTCF_PE_ChIP_chr22_50k.bam
  28 CTRLPE=CTCF_PE_CTRL_chr22_50k.bam
  29
  30 CHIPBEDPE=CTCF_PE_ChIP_chr22_50k.bedpe.gz
  31 CTRLBEDPE=CTCF_PE_CTRL_chr22_50k.bedpe.gz
  32
  33 CHIPCONTIGS50K=contigs50k.bed.gz
  34
  35 CHIPBIGSPEEDTEST=CTCF_12878_5M.bed.gz
  36 CTRLBIGSPEEDTEST=input_12878_5M.bed.gz
  37
  38 CALLVARPEAK=callvar_testing.narrowPeak
  39
  40 ATACSEQBAM=yeast_500k_SRR1822137.bam
  41
  42 # callpeak
  43 echo "1. callpeak"
  44 echo "1.1 callpeak narrow"
  45
  46 mkdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow
  47
  48 macs3 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_narrow0 -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow --cutoff-analysis &> ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0.log
  49 macs3 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_narrow1 -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow --d-min 15 --call-summits &> ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow1.log
  50 macs3 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_narrow2 -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow --nomodel --extsize 100 &> ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow2.log
  51 macs3 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_narrow3 -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow --nomodel --extsize 100 --shift -50 &> ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow3.log
  52 macs3 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_narrow4 -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow --nomodel --nolambda --extsize 100 --shift -50 &> ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow4.log
  53 macs3 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_narrow5 -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow --scale-to large &> ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow5.log
  54
  55 echo "1.2 callpeak broad"
  56 mkdir ${OUTPUTDIR_PREFIX}_run_callpeak_broad
  57
  58 macs3 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_broad -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_broad --broad &> ${OUTPUTDIR_PREFIX}_run_callpeak_broad/run_callpeak_broad.log
  59
  60 echo "1.3 callpeak on PE narrow/broad"
  61
  62 mkdir  ${OUTPUTDIR_PREFIX}_run_callpeak_pe_narrow
  63
  64 macs3 callpeak -g 52000000 -f BAMPE -t $CHIPPE -c $CTRLPE -n run_callpeak_bampe_narrow -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_pe_narrow --call-summits &> ${OUTPUTDIR_PREFIX}_run_callpeak_pe_narrow/run_callpeak_bampe_narrow.log
  65 macs3 callpeak -g 52000000 -f BEDPE -t $CHIPBEDPE -c $CTRLBEDPE -n run_callpeak_bedpe_narrow -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_pe_narrow --call-summits &> ${OUTPUTDIR_PREFIX}_run_callpeak_pe_narrow/run_callpeak_bedpe_narrow.log
  66 macs3 callpeak -g 52000000 -f BEDPE -t $CHIPBEDPE -n run_callpeak_pe_narrow_onlychip -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_pe_narrow &> ${OUTPUTDIR_PREFIX}_run_callpeak_pe_narrow/run_callpeak_pe_narrow_onlychip.log
  67
  68 mkdir  ${OUTPUTDIR_PREFIX}_run_callpeak_pe_broad
  69
  70 macs3 callpeak -g 52000000 -f BAMPE -t $CHIPPE -c $CTRLPE -n run_callpeak_bampe_broad -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_pe_broad --broad &> ${OUTPUTDIR_PREFIX}_run_callpeak_pe_broad/run_callpeak_bampe_broad.log
  71 macs3 callpeak -g 52000000 -f BEDPE -t $CHIPBEDPE -c $CTRLBEDPE -n run_callpeak_bedpe_broad -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_pe_broad --broad &> ${OUTPUTDIR_PREFIX}_run_callpeak_pe_broad/run_callpeak_bedpe_broad.log
  72
  73 # pileup
  74 echo "2. pileup"
  75
  76 mkdir ${OUTPUTDIR_PREFIX}_run_pileup
  77
  78 macs3 pileup -f BED -i $CHIP --extsize 200 --outdir ${OUTPUTDIR_PREFIX}_run_pileup -o run_pileup_ChIP.bed.bdg &> ${OUTPUTDIR_PREFIX}_run_pileup/run_pileup_ChIP.bed.log
  79 macs3 pileup -f BED -i $CTRL --extsize 200 --outdir ${OUTPUTDIR_PREFIX}_run_pileup -o run_pileup_CTRL.bed.bdg &> ${OUTPUTDIR_PREFIX}_run_pileup/run_pileup_CTRL.bed.log
  80
  81 macs3 pileup -f BAMPE -i $CHIPPE --outdir ${OUTPUTDIR_PREFIX}_run_pileup -o run_pileup_ChIPPE.bampe.bdg &> ${OUTPUTDIR_PREFIX}_run_pileup/run_pileup_ChIPPE.bampe.log
  82 macs3 pileup -f BAMPE -i $CTRLPE --outdir ${OUTPUTDIR_PREFIX}_run_pileup -o run_pileup_CTRLPE.bampe.bdg &> ${OUTPUTDIR_PREFIX}_run_pileup/run_pileup_CTRLPE.bampe.log
  83
  84 macs3 pileup -f BEDPE -i $CHIPBEDPE --outdir ${OUTPUTDIR_PREFIX}_run_pileup -o run_pileup_ChIPPE.bedpe.bdg &> ${OUTPUTDIR_PREFIX}_run_pileup/run_pileup_ChIPPE.bedpe.log
  85 macs3 pileup -f BEDPE -i $CTRLBEDPE --outdir ${OUTPUTDIR_PREFIX}_run_pileup -o run_pileup_CTRLPE.bedpe.bdg &> ${OUTPUTDIR_PREFIX}_run_pileup/run_pileup_CTRLPE.bedpe.log
  86
  87 # filterdup
  88 echo "3. filterdup"
  89
  90 mkdir ${OUTPUTDIR_PREFIX}_run_filterdup
  91
  92 macs3 filterdup -g 52000000 -i $CHIP --outdir ${OUTPUTDIR_PREFIX}_run_filterdup -o run_filterdup_result.bed --dry-run &> ${OUTPUTDIR_PREFIX}_run_filterdup/run_filterdup_d.log
  93 macs3 filterdup -g 52000000 -i $CHIP --outdir ${OUTPUTDIR_PREFIX}_run_filterdup -o run_filterdup_result.bed &> ${OUTPUTDIR_PREFIX}_run_filterdup/run_filterdup.log
  94
  95 macs3 filterdup -g 52000000 -i $CHIPPE -f BAMPE --outdir ${OUTPUTDIR_PREFIX}_run_filterdup -o run_filterdup_result_pe.bedpe --dry-run &> ${OUTPUTDIR_PREFIX}_run_filterdup/run_filterdup_pe_d.log
  96 macs3 filterdup -g 52000000 -i $CHIPPE -f BAMPE --outdir ${OUTPUTDIR_PREFIX}_run_filterdup -o run_filterdup_result_pe.bedpe &> ${OUTPUTDIR_PREFIX}_run_filterdup/run_filterdup_pe.log
  97
  98 # predictd
  99 echo "4. predictd"
 100
 101 mkdir ${OUTPUTDIR_PREFIX}_run_predictd
 102
 103 macs3 predictd -i $CHIPPE -f BAMPE --outdir ${OUTPUTDIR_PREFIX}_run_predictd &> ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd_bampe.log
 104 grep "Average insertion length" ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd_bampe.log | perl -pe 's/^.*\s(\d+)\sbps/$1/' > ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd_bampe.txt
 105
 106 macs3 predictd -i $CHIPBEDPE -f BEDPE --outdir ${OUTPUTDIR_PREFIX}_run_predictd &> ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd_bedpe.log
 107 grep "Average insertion length" ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd_bedpe.log | perl -pe 's/^.*\s(\d+)\sbps/$1/' > ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd_bedpe.txt
 108
 109 macs3 predictd -g 52000000 -i $CHIP --d-min 10 --outdir ${OUTPUTDIR_PREFIX}_run_predictd --rfile run_predictd.R &> ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd.log
 110 grep "predicted fragment length" ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd.log | perl -pe 's/^.*\s(\d+)\sbps/$1/' > ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd.txt
 111 grep "alternative fragment length" ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd.log | perl -pe 's/^.*\s(\S+)\sbps/$1/' >> ${OUTPUTDIR_PREFIX}_run_predictd/run_predictd.txt
 112
 113 # randsample
 114 echo "5. randsample"
 115
 116 mkdir ${OUTPUTDIR_PREFIX}_run_randsample
 117
 118 macs3 randsample -i $CHIP -n 10000 --seed 31415926 --outdir ${OUTPUTDIR_PREFIX}_run_randsample -o run_randsample.bed &> ${OUTPUTDIR_PREFIX}_run_randsample/run_randsample.log
 119
 120 macs3 randsample -f BAMPE -i $CHIPPE -n 10000 --seed 31415926 --outdir ${OUTPUTDIR_PREFIX}_run_randsample -o run_randsample_bampe.bedpe &> ${OUTPUTDIR_PREFIX}_run_randsample/run_randsample_bampe.log
 121
 122 macs3 randsample -f BEDPE -i $CHIPBEDPE -n 10000 --seed 31415926 --outdir ${OUTPUTDIR_PREFIX}_run_randsample -o run_randsample_bedpe.bedpe &> ${OUTPUTDIR_PREFIX}_run_randsample/run_randsample_bedpe.log
 123
 124 # refinepeak
 125 echo "6. refinepeak"
 126
 127 mkdir ${OUTPUTDIR_PREFIX}_run_refinepeak
 128
 129 macs3 refinepeak -b ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_peaks.narrowPeak -i $CHIP --outdir ${OUTPUTDIR_PREFIX}_run_refinepeak --o-prefix run_refinepeak_w_prefix &> ${OUTPUTDIR_PREFIX}_run_refinepeak/run_refinepeak_w_prefix.log
 130
 131 macs3 refinepeak -b ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_peaks.narrowPeak -i $CHIP --outdir ${OUTPUTDIR_PREFIX}_run_refinepeak -o run_refinepeak_w_ofile.bed &> ${OUTPUTDIR_PREFIX}_run_refinepeak/run_refinepeak_w_ofile.log
 132
 133 # bdgcmp
 134 echo "7. bdgcmp"
 135
 136 mkdir ${OUTPUTDIR_PREFIX}_run_bdgcmp
 137
 138 macs3 bdgcmp -t ${OUTPUTDIR_PREFIX}_run_pileup/run_pileup_ChIP.bed.bdg -c ${OUTPUTDIR_PREFIX}_run_pileup/run_pileup_CTRL.bed.bdg  -m ppois FE -p 1 --outdir ${OUTPUTDIR_PREFIX}_run_bdgcmp --o-prefix run_bdgcmp &> ${OUTPUTDIR_PREFIX}_run_bdgcmp/run_bdgcmp.log
 139
 140 # bdgpeakcall
 141 echo "8. bdgpeakcall"
 142
 143 mkdir ${OUTPUTDIR_PREFIX}_run_bdgpeakcall
 144
 145 macs3 bdgpeakcall -i ${OUTPUTDIR_PREFIX}_run_bdgcmp/run_bdgcmp_FE.bdg -c 2 --outdir ${OUTPUTDIR_PREFIX}_run_bdgpeakcall --o-prefix run_bdgpeakcall_w_prefix &> ${OUTPUTDIR_PREFIX}_run_bdgpeakcall/run_bdgpeakcall_w_prefix.log
 146
 147 macs3 bdgpeakcall -i ${OUTPUTDIR_PREFIX}_run_bdgcmp/run_bdgcmp_FE.bdg -c 2 --outdir ${OUTPUTDIR_PREFIX}_run_bdgpeakcall -o run_bdgpeakcall_cutoff.txt --cutoff-analysis &> ${OUTPUTDIR_PREFIX}_run_bdgpeakcall/run_bdgpeakcall_cutoff.log
 148
 149 # bdgbroadcall
 150 echo "9. bdgbroadcall"
 151
 152 mkdir ${OUTPUTDIR_PREFIX}_run_bdgbroadcall
 153
 154 macs3 bdgbroadcall -i ${OUTPUTDIR_PREFIX}_run_bdgcmp/run_bdgcmp_FE.bdg -c 2 -C 1.5 --outdir ${OUTPUTDIR_PREFIX}_run_bdgbroadcall --o-prefix run_bdgbroadcall_w_prefix &> ${OUTPUTDIR_PREFIX}_run_bdgbroadcall/run_bdgbroadcall_w_prefix.log
 155
 156 # bdgdiff
 157 echo "10. bdgdiff"
 158
 159 mkdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow_revert
 160 mkdir ${OUTPUTDIR_PREFIX}_run_bdgdiff
 161
 162 macs3 callpeak -g 10000000 --nomodel --extsize 250 -c $CHIP -t $CTRL -n run_callpeak_narrow_revert -B --outdir ${OUTPUTDIR_PREFIX}_run_callpeak_narrow_revert &> ${OUTPUTDIR_PREFIX}_run_callpeak_narrow_revert/run_callpeak_narrow_revert.log
 163
 164 macs3 bdgdiff --t1 ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_treat_pileup.bdg --c1 ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_control_lambda.bdg --t2 ${OUTPUTDIR_PREFIX}_run_callpeak_narrow_revert/run_callpeak_narrow_revert_treat_pileup.bdg --c2 ${OUTPUTDIR_PREFIX}_run_callpeak_narrow_revert/run_callpeak_narrow_revert_control_lambda.bdg --o-prefix run_bdgdiff_prefix --outdir ${OUTPUTDIR_PREFIX}_run_bdgdiff &> ${OUTPUTDIR_PREFIX}_run_bdgdiff/run_bdgdiff_w_prefix.log
 165
 166 macs3 bdgdiff --t1 ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_treat_pileup.bdg --c1 ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_control_lambda.bdg --t2 ${OUTPUTDIR_PREFIX}_run_callpeak_narrow_revert/run_callpeak_narrow_revert_treat_pileup.bdg --c2 ${OUTPUTDIR_PREFIX}_run_callpeak_narrow_revert/run_callpeak_narrow_revert_control_lambda.bdg -o cond1.bed cond2.bed common.bed --outdir ${OUTPUTDIR_PREFIX}_run_bdgdiff &> ${OUTPUTDIR_PREFIX}_run_bdgdiff/run_bdgdiff_w_o_file.log
 167
 168 # cmbreps
 169 echo "11. cmbreps"
 170
 171 mkdir ${OUTPUTDIR_PREFIX}_run_cmbreps
 172
 173 macs3 cmbreps -i ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_treat_pileup.bdg ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_control_lambda.bdg ${OUTPUTDIR_PREFIX}_run_bdgcmp/run_bdgcmp_ppois.bdg -m max -o run_cmbreps_max.bdg --outdir ${OUTPUTDIR_PREFIX}_run_cmbreps &> ${OUTPUTDIR_PREFIX}_run_cmbreps/run_cmbreps_max.log
 174 macs3 cmbreps -i ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_treat_pileup.bdg ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_control_lambda.bdg ${OUTPUTDIR_PREFIX}_run_bdgcmp/run_bdgcmp_ppois.bdg -m mean -o run_cmbreps_mean.bdg --outdir ${OUTPUTDIR_PREFIX}_run_cmbreps &> ${OUTPUTDIR_PREFIX}_run_cmbreps/run_cmbreps_mean.log
 175 macs3 cmbreps -i ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_treat_pileup.bdg ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_control_lambda.bdg ${OUTPUTDIR_PREFIX}_run_bdgcmp/run_bdgcmp_ppois.bdg -m fisher -o run_cmbreps_fisher.bdg --outdir ${OUTPUTDIR_PREFIX}_run_cmbreps &> ${OUTPUTDIR_PREFIX}_run_cmbreps/run_cmbreps_fisher.log
 176
 177 # bdgopt
 178 echo "12. bdgopt"
 179
 180 mkdir ${OUTPUTDIR_PREFIX}_run_bdgopt
 181
 182 macs3 bdgopt -m min -p 10 -i ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_treat_pileup.bdg -o run_bdgopt_min.bdg --outdir ${OUTPUTDIR_PREFIX}_run_bdgopt &> ${OUTPUTDIR_PREFIX}_run_bdgopt/run_bdgopt_min.log
 183
 184 macs3 bdgopt -m max -p 2 -i ${OUTPUTDIR_PREFIX}_run_callpeak_narrow/run_callpeak_narrow0_treat_pileup.bdg -o run_bdgopt_max.bdg --outdir ${OUTPUTDIR_PREFIX}_run_bdgopt &> ${OUTPUTDIR_PREFIX}_run_bdgopt/run_bdgopt_max.log
 185
 186 # callvar
 187 echo "13. callvar"
 188
 189 mkdir ${OUTPUTDIR_PREFIX}_run_callvar
 190
 191 macs3 callvar -b ${CALLVARPEAK} -t ${CHIPPE} -c ${CTRLPE} -o ${OUTPUTDIR_PREFIX}_run_callvar/PEsample.vcf &> ${OUTPUTDIR_PREFIX}_run_callvar/run_callvar_PE.log
 192
 193 # test large amount of contigs
 194 echo "14. 50k contigs with buffersize"
 195
 196 mkdir ${OUTPUTDIR_PREFIX}_run_50kcontigs
 197
 198 echo "14.1 callpeak"
 199 macs3 callpeak -g 10000000 -t $CHIPCONTIGS50K -n run_callpeak_50kcontigs --outdir ${OUTPUTDIR_PREFIX}_run_50kcontigs --buffer-size 1000 --nomodel --extsize 200 &> ${OUTPUTDIR_PREFIX}_run_50kcontigs/run_callpeak_50kcontigs.log
 200
 201 echo "14.2 filterdup"
 202 macs3 filterdup -g 10000000 -i $CHIPCONTIGS50K --outdir ${OUTPUTDIR_PREFIX}_run_50kcontigs -o run_filterdup_result.bed --buffer-size 1000 &> ${OUTPUTDIR_PREFIX}_run_50kcontigs/run_filterdup_50kcontigs.log
 203
 204 echo "14.3 pileup"
 205 macs3 pileup -f BED -i $CHIPCONTIGS50K --extsize 200 --outdir ${OUTPUTDIR_PREFIX}_run_50kcontigs -o run_pileup_ChIP.bed.bdg --buffer-size 1000 &> ${OUTPUTDIR_PREFIX}_run_50kcontigs/run_pileup_ChIP.bed.log
 206
 207 echo "14.4 randsample"
 208 macs3 randsample -i $CHIPCONTIGS50K -n 100000 --seed 31415926 --outdir ${OUTPUTDIR_PREFIX}_run_50kcontigs -o run_randsample.bed --buffer-size 1000 &> ${OUTPUTDIR_PREFIX}_run_50kcontigs/run_randsample.log
 209
 210 echo "15. skip hmmratac"
 211 #mkdir ${OUTPUTDIR_PREFIX}_run_hmmratac
 212
 213 #macs3 hmmratac -b $ATACSEQBAM -n hmmratac_yeast500k --outdir ${OUTPUTDIR_PREFIX}_run_hmmratac &> ${OUTPUTDIR_PREFIX}_run_hmmratac/run_hmmratac.log
 214
 215 echo "16. search for errors or warnings in log files"
 216 flag=0
 217 for i in `ls ${OUTPUTDIR_PREFIX}_run_*/*.log`;do
 218     echo " checking $i..."
 219     egrep -i "error|warning" $i;
 220     if [[ $? == 0 ]];then
 221         echo " ... error/warning found!"
 222         echo "the log file:"
 223         cat $i;
 224         let "flag=1";
 225     else
 226         echo " ... clear!"
 227     fi
 228 done;
 229
 230 if [[ $flag == 1 ]]; then
 231     echo " Error or Warning can be found! Quit the test!"
 232     exit 1;
 233 fi
 234
 235 echo "17. compare with standard outputs"
 236
 237 flag=0
 238 # we do not check the consistency of random subsampling results and hmmratac on non-x86 arch
 239 subfolders=(50kcontigs bdgbroadcall bdgcmp bdgdiff bdgpeakcall callpeak_broad callpeak_narrow callpeak_narrow_revert callpeak_pe_broad callpeak_pe_narrow cmbreps filterdup pileup refinepeak bdgopt predictd callvar)  # hmmratac)
 240
 241 m=0
 242 n=0
 243 for i in ${subfolders[@]};do
 244     let "m+=1"
 245     let "n=0"
 246     for j in `ls standard_results_${i}/*`; do
 247         k=`basename $j`
 248         let "n+=1"
 249         echo "16.${m}.${n} checking $i $k ..."
 250         fq=${OUTPUTDIR_PREFIX}_run_${i}/${k}
 251         fs=standard_results_${i}/${k}
 252         if [ "${REPLACE}" = "Y" ]; then
 253             cp $fq $fs
 254             echo " ... replaced!"
 255         else
 256             sort $fq| grep -v ^# > tmp_fq.txt
 257             sort $fs| grep -v ^# > tmp_fs.txt
 258             d=`diff tmp_fq.txt tmp_fs.txt`
 259             if [ -z "$d" ]; then
 260                 echo " ... success!"
 261             else
 262                 echo " ... failed! Difference:"
 263                 diff tmp_fq.txt tmp_fs.txt | head -10
 264                 let "flag=1";
 265             fi
 266         fi
 267     done
 268 done
 269 rm -f tmp_fq.txt tmp_fs.txt
 270
 271 # exit with 1 if test fails
 272 if [ $flag -eq 1 ];then
 273     exit $flag;
 274 fi
 275
 276 echo "17. brief speed test"
 277
 278 mkdir ${OUTPUTDIR_PREFIX}_speedtest
 279 macs3 callpeak -t CTCF_12878_5M.bed.gz -c Input_12878_5M.bed.gz -n speedtest -B --outdir ${OUTPUTDIR_PREFIX}_speedtest &> ${OUTPUTDIR_PREFIX}_speedtest/speedtest.log &
 280 # monitor the macs3 callpeak run and output CPU and mem usage
 281 ./prockreport 0.5 $!
 282 wait;
 283
 284 # END of test