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#include "SortingCount.h"
#include "inttypes.h"
#include <sys/resource.h> // for getrlimit()
#if OMP
#include "omp.h"
#endif
#define SINGLE_BAR 1
#define SEP
bool clear_cache = false; // clear file cache from memory (for timing only)
bool hybrid_mode = false;
bool use_hashing = true; // use hashing instead of sorting (better control of memory)
float load_factor = 0.7;
bool separate_count = true ; // count separately the multiple read sets, only works with use_hashing, needs define SEP and use_hashing=true
bool use_compressed_reads = true ; // true; // write compressed read file
int optimism = 1; // optimism == 1 mean that we garantee worst case the memory usage, any value above assumes that, on average, a k-mer will be seen 'optimism' times
bool output_histo;
// main k-mer counting function, shared between minia and dsk
// verbose == 0 : stderr progress bar
// verbose >= 1 : print basic status
// verbose >= 2 : print extra partition information
// write_count == True: include kmer count in results file, in that form:
// - save kmer count for each kmer in the resulting binary file
// - the very first four bytes of the result file are the kmer length
void sorting_count(Bank *Sequences, char *prefix, int max_memory, int max_disk_space, bool write_count, int verbose, bool skip_binary_conversion)
{
// create a temp dir from the prefix
char temp_dir[1024];
sprintf(temp_dir,"%s_temp",prefix);
// clear the temp folder (needs to be done before estimating disk space)
DIR* dp;
struct dirent* ep;
char p_buf[512] = {0};
dp = opendir(temp_dir);
while ( (dp != NULL) && ((ep = readdir(dp)) != NULL)) {
sprintf(p_buf, "%s/%s", temp_dir, ep->d_name);
remove(p_buf);
}
if(dp != NULL)
closedir(dp);
if (max_disk_space == 0)
{
// default max disk space
struct statvfs buffer ;
char current_path[1000];
getcwd(current_path,sizeof(current_path));
// int ret =
statvfs(current_path, &buffer);
uint32_t available = (uint32_t)(((double)buffer.f_bavail * (double)buffer.f_bsize) / 1024.0 / 1024.0);
printf("Available disk space in %s: %d MB\n",current_path,available); // not working in osx (is that a TODO then?)
uint32_t input_size = max(1, (int)(( (double)(Sequences->filesizes) ) / 1024.0 / 1024.0));
max_disk_space = min(available/2, input_size);
}
if (max_disk_space == 0) // still 0?
max_disk_space = 10000; // = default for osx
// estimate number of iterations
uint64_t volume = Sequences->estimate_kmers_volume(sizeKmer);
uint32_t nb_passes = ( volume / max_disk_space ) + 1;
int nb_threads=1;
#if OMP
use_compressed_reads = true;
nb_threads = 8;
max_memory /= nb_threads;
max_memory = max (max_memory,1);
#endif
// temp bugfix: don't use compressed reads for long reads
if (Sequences->estimate_max_readlen() > 1000000)
use_compressed_reads = false;
uint64_t volume_per_pass;
uint32_t nb_partitions;
// loop to lower the number of partitions below the maximum number of simulatenously open files
do
{
volume_per_pass = volume / nb_passes;
nb_partitions = ( volume_per_pass / max_memory ) + 1;
// if partitions are hashed instead of sorted, adjust for load factor
// (as in the worst case, all kmers in the partition are distinct and partition may be slightly bigger due to hash-repartition)
if (use_hashing)
{
nb_partitions = (uint32_t) ceil((float) nb_partitions / load_factor);
nb_partitions = ((nb_partitions * OAHash::size_entry()) + sizeof(key_type)-1) / sizeof(key_type); // also adjust for hash overhead
nb_partitions = max((int)(nb_partitions/optimism), 1);
if (verbose)
printf("Updated number of partitions for hash-based k-mer counting: %d\n",nb_partitions);
}
// round nb_partitions to mulitple of nthreads, for better perf
// nb_partitions = ((nb_partitions + nb_threads - 1) / nb_threads) * nb_threads;
if (verbose)
printf("Estimate of number of partitions: %d, number of passes: %d\n",nb_partitions, nb_passes);
// get max number of open files
struct rlimit lim;
int max_open_files = 1000;
int err = getrlimit(RLIMIT_NOFILE, &lim);
if (err == 0)
max_open_files = lim.rlim_cur / 2;
if (nb_partitions >= max_open_files)
{
if (verbose)
printf("Number of partitions higher than max. number of open files (%d), need to increase the number of passes\n", max_open_files);
nb_passes++;
}
else
break;
}
while (1);
// volume / (sizeof(kmer_type)*4) is approx size of read file stored in binary, read nb_passes -1 times
uint64_t total_IO = volume * 2LL * 1024LL*1024LL ;// in bytes + nb_passes * ( volume / (sizeof(kmer_type)*4) ) ; // in bytes
uint64_t temp_IO = 0;
//if (nb_passes==1) use_compressed_reads=false;
BinaryBankConcurrent * redundant_partitions_file[nb_partitions];
char redundant_filename[nb_partitions][256];
kmer_type kmer;
int max_read_length = KMERSBUFFER_MAX_READLEN;
kmer_type * kmer_table_seq = (kmer_type * ) malloc(sizeof(kmer_type)*max_read_length); ;
fprintf(stderr,"Sequentially counting ~%llu MB of kmers with %d partition(s) and %d passes using %d thread(s), ~%d MB of memory and ~%d MB of disk space\n", (unsigned long long)volume, nb_partitions,nb_passes, nb_threads, max_memory * nb_threads, max_disk_space);
STARTWALL(count);
mkdir(temp_dir, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
BinaryBankConcurrent * SolidKmers = new BinaryBankConcurrent(return_file_name(solid_kmers_file),sizeof(kmer),true,nb_threads);
if (write_count)
{
// write k-mer nbits as the first 4 bytes; and actual k-mer size as the next 4 bits
uint32_t kmer_nbits = sizeof(kmer) * 8;
SolidKmers->write_buffered(&kmer_nbits, 4,0);
SolidKmers->write_buffered(&sizeKmer, 4,0);
SolidKmers->flush(0);
}
int64_t estimated_NbReads = Sequences->estimate_nb_reads(); // only used in progress prints
char * rseq;
int readlen;
int64_t NbSolid = 0;
int64_t * NbSolid_omp = (int64_t *) calloc(nb_threads,sizeof(int64_t));
#ifdef SEP
long total_kmers_per_partition[nb_partitions]; //guillaume probably commented it because updating this variable would require synchronization
for (int jj=0; jj<nb_partitions; jj++) {
total_kmers_per_partition[jj]=0;
}
long kmers_perparti_perfile[nb_partitions][1000];//store cumulated counter
for (int ii=0; ii<nb_partitions; ii++) {
for (int jj=0; jj<1000; jj++) {
kmers_perparti_perfile[ii][jj]=0;
}
}
#endif
long distinct_kmers_per_partition[nb_partitions];
uint64_t * histo_count = (uint64_t *) calloc(10001,sizeof(uint64_t));
#if OMP
printf("coucou coucou coucou \n \n \n");
uint64_t ** histo_count_omp = (uint64_t **) calloc(nb_threads,sizeof(uint64_t *));
for(int ii=0;ii<nb_threads;ii++)
{
histo_count_omp[ii]= (uint64_t *) calloc(10001,sizeof(uint64_t));
}
#endif
//start by the conversion of the file to binary format
BinaryReads * binread = NULL;
if (skip_binary_conversion)
{
binread = new BinaryReads(return_file_name(binary_read_file),false);
binread->close();
}
if(use_compressed_reads && (!skip_binary_conversion))
{
char * pt_begin;
int idx =0 ;
int64_t NbRead = 0;
Progress progress_conversion;
// progress_conversion.timer_mode=1; // to switch to timer mode (show elapsed and estimated remaining time)
progress_conversion.init(estimated_NbReads,"First step: Converting input file into Binary format");
binread = new BinaryReads(return_file_name(binary_read_file),true);
#ifdef SEP
int file_id =0;
int prev_file_id =0;
#endif
Sequences->rewind_all();
while(1)
{
#ifdef SEP
if(! Sequences->get_next_seq(&rseq,&readlen,&file_id)) break; // read original fasta file
if(separate_count && (file_id != prev_file_id))
{
//printf("new file \n");
prev_file_id = file_id;
binread->mark_newfile();
}
#else
if(! Sequences->get_next_seq(&rseq,&readlen)) break; // read original fasta file
#endif
if(readlen > max_read_length) // realloc kmer_table_seq if needed
{
max_read_length = 2*readlen;
kmer_table_seq = (kmer_type * ) realloc(kmer_table_seq,sizeof(kmer_type)*max_read_length);
}
pt_begin = rseq;
//should be ok
while (pt_begin < (rseq+ readlen))
{
idx=0; // start a new read
//skips NN
while (*pt_begin =='N' && pt_begin < (rseq+ readlen))
{
pt_begin ++;
}
// goes to next N or end of seq
while ( (pt_begin[idx] !='N') && ((pt_begin +idx) < (rseq+ readlen)) )
{
idx++;
}
//we have a seq beginning at pt_begin of size idx ,without any N, will be treated as a read:
binread->write_read(pt_begin,idx);
pt_begin += idx;
}
// binread->write_read(rseq,readlen);
NbRead++;
if ((NbRead%10000)==0)
{
progress_conversion.inc(10000);
}
}
progress_conversion.finish();
binread->close();
}
///fin conversion
if (clear_cache)
{
#ifdef OSX
system("purge");
#else
system("echo 3 > /proc/sys/vm/drop_caches");
#endif
}
#if SINGLE_BAR
Progress progress;
char message[1000];
sprintf(message,"Counting kmers");
progress.timer_mode=1;
if (verbose == 0 )
progress.init(total_IO,message);
#endif
// nb_passes = how many times we will traverse the whole reads file (has an influence on temp disk space)
for (uint32_t current_pass = 0; current_pass < nb_passes; current_pass ++)
{
#ifdef SEP
if(separate_count)
{
for (int jj=0; jj<nb_partitions; jj++) {
total_kmers_per_partition[jj]=0;
}
for (int ii=0; ii<nb_partitions; ii++) {
for (int jj=0; jj<1000; jj++) {
kmers_perparti_perfile[ii][jj]=0;
}
}
}
#endif
if(use_compressed_reads ) //open binary reads for reading
binread->open(false);
STARTWALL(debpass);
STARTWALL(debw);
for (uint32_t p=0;p<nb_partitions;p++)
{
sprintf(redundant_filename[p],"%s/partition%d.redundant_kmers",temp_dir,p);
redundant_partitions_file[p] = new BinaryBankConcurrent (redundant_filename[p],sizeof(kmer_type),true, nb_threads);
distinct_kmers_per_partition[p]=0;
}
// partitioning redundant kmers
Sequences->rewind_all();
#if !SINGLE_BAR
Progress progress;
progress.timer_mode=1; // to switch to timer mode (show elapsed and estimated remaining time)
char message[1000];
sprintf(message,"Pass %d/%d, Step 1: partitioning",current_pass+1,nb_passes);
if (verbose == 0 )
progress.init(estimated_NbReads,message);
#endif
int file_id=0;
//current_pass> 0 &&
#if OMP
#pragma omp parallel if(use_compressed_reads && ! separate_count) num_threads(nb_threads)
#endif
{
int64_t nbkmers_written =0;
int tid =0;
int64_t NbRead = 0;
int64_t nread =0;
int64_t tempread =0;
#if OMP
tid = omp_get_thread_num();
#endif
int nreads_in_buffer= 1000;
KmersBuffer * kbuff =NULL;
if(use_compressed_reads)
{
kbuff = new KmersBuffer (binread, 1000000, nreads_in_buffer); //buffer size (in nb of kmers), seq per task // the buffer is per thread
kbuff->binary_read_file = binread->binary_read_file;
}
kmer_type * kmer_table ;
while(1)
{
//read the fasta file
if(use_compressed_reads) // && current_pass>0
{
nread = kbuff->readkmers();
#ifdef SEP
if(separate_count && (nread == -2))
{
//printf("New file notified, filling parti\n");
for (int kk=0; kk< nb_partitions; kk++) {
kmers_perparti_perfile[kk][file_id] = total_kmers_per_partition [kk];
//printf(".. total_kmers_per_partition[%i] = %li\n",kk, total_kmers_per_partition [kk]);
}
file_id++;
continue;
}
#endif
if(nread < 0) break;
NbRead+= nread;
tempread+= nread;
}
else
{
if(! Sequences->get_next_seq(&rseq,&readlen)) break; // read original fasta file
if(readlen > max_read_length) // realloc kmer_table_seq if needed
{
max_read_length = 2*readlen;
kmer_table_seq = (kmer_type * ) realloc(kmer_table_seq,sizeof(kmer_type)*max_read_length);
}
}
// if(use_compressed_reads ) //write compressed read file at first pass //&& current_pass==0
// binread->write_read(rseq,readlen);
int i;
int nbkmers =readlen-sizeKmer+1;
if( use_compressed_reads) //current_pass >0 &&
{
nbkmers = kbuff->nkmers;
kmer_table = kbuff->kmers_buffer;
// printf("nb kmers read %lli \n",nbkmers);
// NbRead+= nreads_in_buffer;
}
else //old fashion
{
compute_kmer_table_from_one_seq(readlen,rseq,kmer_table_seq);
nbkmers =readlen-sizeKmer+1;
kmer_table = kmer_table_seq;
NbRead++;
}
//printf("Encountering empty block \n");
nbkmers_written= 0;
//compute the kmers stored in the buffer kmer_table
for (i=0; i<nbkmers; i++)
{
kmer_type lkmer;
// kmer = extractKmerFromRead(rseq,i,&graine,&graine_revcomp);
lkmer = kmer_table[i];
// some hashing to uniformize repartition
kmer_type kmer_hash = lkmer ^ (lkmer >> 14);
kmer_hash = (~kmer_hash) + (kmer_hash << 18);
kmer_hash = kmer_hash ^ (kmer_hash >> 31);
kmer_hash = kmer_hash * 21;
kmer_hash = kmer_hash ^ (kmer_hash >> 11);
kmer_hash = kmer_hash + (kmer_hash << 6);
kmer_hash = kmer_hash ^ (kmer_hash >> 22);
// check if this kmer should be included in the current pass
if ((kmer_hash % nb_passes ) != current_pass)
continue;
kmer_type reduced_kmer = kmer_hash / nb_passes;
int p;// compute in which partition this kmer falls into
#ifdef _ttmath
(reduced_kmer % nb_partitions).ToInt(p);
#else
p = reduced_kmer % nb_partitions;
#endif
nbkmers_written++;
redundant_partitions_file[p]->write_element_buffered(&lkmer,tid); // save this kmer to the right partition file
#ifdef SEP
if(separate_count)
total_kmers_per_partition[p]++; // guillaume probably commented it because updating this variable would require synchronization
#endif
}
//NbRead++;
#if SINGLE_BAR
if(verbose==0)
{
if (nb_threads == 1)
progress.inc(nbkmers_written * sizeof(kmer_type));
else
progress.inc(nbkmers_written * sizeof(kmer_type),tid);
}
#endif
// if ((NbRead%10000)==0)
if(tempread> 10000)
{
tempread -= 10000;
if (verbose)
fprintf (stderr,"%cPass %d/%d, loop through reads to separate (redundant) kmers into partitions, processed %lluM reads out of %lluM",13,current_pass+1,nb_passes,(unsigned long long)(NbRead/1000/1000),(unsigned long long)(estimated_NbReads/1000/1000));
#if !SINGLE_BAR
else
if (nb_threads == 1)
progress.set(NbRead);
else
progress.inc(10000,tid);
#endif
}
} //end while
if(use_compressed_reads)
delete kbuff;
} // end OMP
#if !SINGLE_BAR
if (verbose == 0)
{
if (nb_threads == 1)
progress.finish();
else
progress.finish_threaded(); // here only one thread
sprintf(message,"Pass %d/%d, Step 2: computing kmer count per partition",current_pass+1,nb_passes);
progress.init(nb_partitions+1,message);
}
#endif
if (verbose)fprintf(stderr,"\n");
if (verbose >= 2)
{
STOPWALL(debw,"Writing redundant kmers");
}
STARTWALL(debtri);
// close partitions and open them for reading
for (uint32_t p=0;p<nb_partitions;p++)
{
redundant_partitions_file[p]->close();
redundant_partitions_file[p]->open(false);
}
// for better timing: clear the file cache, since the partitions may still be in memory, that's unfair to low mem machines
if (clear_cache)
{
#ifdef OSX
system("purge");
#else
system("echo 3 > /proc/sys/vm/drop_caches");
#endif
}
//quick and dirty parall with omp, testing
//todo if we want omp and histo : separate histo_count tab per thread that needs to be merged at the end
// TODO to guillaume: remove that todo above, because it is done, right?
#if OMP
//omp_set_numthreads(2); //num_threads(2) //if(!output_histo) num_threads(nb_threads)
#pragma omp parallel for if (! separate_count) private (p) num_threads(nb_threads)
#endif
// load, sort each partition to output solid kmers
for (int p=0;p<nb_partitions;p++)
{
kmer_type lkmer;
bool use_hashing_for_this_partition = use_hashing;
if(hybrid_mode)
{
// printf("max mem %i MB , parti size %i MB\n",max_memory,(redundant_partitions_file[p]->nb_elements()*sizeof(kmer_type))/1024LL/1024LL);
if( (redundant_partitions_file[p]->nb_elements()*sizeof(kmer_type)) < (max_memory*1024LL*1024LL) )
use_hashing_for_this_partition = false;
else
use_hashing_for_this_partition = true;
}
int tid =0;
#if OMP
tid = omp_get_thread_num();
#endif
if (use_hashing_for_this_partition)
{
// hash partition and save to solid file
OAHash hash(max_memory*1024LL*1024LL);
uint64_t nkmers_read=0;
uint64_t nkmers_read_all=0;
file_id = 0;
while (redundant_partitions_file[p]->read_element_buffered (&lkmer))
{
hash.increment(lkmer);
nkmers_read++;
#ifdef SEP
nkmers_read_all++;
if( separate_count && (kmers_perparti_perfile[p][file_id]==nkmers_read_all))
{
//printf("Parsing parti .. detected end of file %i at %lli parti %i \n",file_id,nkmers_read_all,p);
file_id++;
//faire raz des cpts < seuil de la hash, devrait etre suffisant ...
hash.start_iterator();
while (hash.next_iterator())
{
if (hash.iterator->value < nks)
{
hash.iterator->value = -1 ; // 0 is not valid in oahash, emulate it with -1
}
}
}
#endif
#if SINGLE_BAR
if(verbose==0 && nkmers_read==10000)
{
if (nb_threads == 1)
progress.inc(nkmers_read*sizeof(kmer_type));
else
progress.inc(nkmers_read*sizeof(kmer_type),tid);
nkmers_read=0;
}
#endif
}
//single bar
if (verbose >= 2)
printf("Pass %d/%d partition %d/%d hash load factor: %0.3f\n",current_pass+1,nb_passes,p+1,nb_partitions,hash.load_factor());
hash.start_iterator();
while (hash.next_iterator())
{
#ifdef SEP
int value = hash.iterator->value;
if(value==-1) value = 0; // desemulate -1
uint_abundance_t abundance = value;
#else
uint_abundance_t abundance = hash.iterator->value;
#endif
if(output_histo)
{
uint_abundance_t saturated_abundance;
saturated_abundance = (abundance >= 10000) ? 10000 : abundance;
#if OMP
histo_count_omp[tid][saturated_abundance]++;
#else
//printf("histo_count 0 1 2 %i %i %i \n",histo_count[0],histo_count[1],histo_count[2]);
histo_count[saturated_abundance]++;
#endif
}
if (abundance >= nks && abundance <= max_couv)
{
SolidKmers->write_element_buffered(&(hash.iterator->key),tid);
NbSolid_omp[tid]++;
if (write_count)
SolidKmers->write_buffered(&abundance, sizeof(abundance),tid, false);
}
distinct_kmers_per_partition[p]++;
}
}
else
{
// sort partition and save to solid file
vector < kmer_type > kmers;
uint64_t nkmers_read=0;
while (redundant_partitions_file[p]->read_element_buffered (&lkmer))
{
kmers.push_back (lkmer);
nkmers_read++;
#if SINGLE_BAR
if(verbose==0 && nkmers_read==10000)
{
if (nb_threads == 1)
progress.inc(nkmers_read*sizeof(kmer_type));
else
progress.inc(nkmers_read*sizeof(kmer_type),tid);
nkmers_read=0;
}
#endif
}
sort (kmers.begin (), kmers.end ());
kmer_type previous_kmer = *(kmers.begin ());
uint_abundance_t abundance = 0;
for (vector < kmer_type >::iterator it = kmers.begin (); it != kmers.end ();
it++)
{
kmer_type current_kmer = *it;
if (current_kmer == previous_kmer)
abundance++;
else
{
if(output_histo)
{
uint_abundance_t saturated_abundance;
saturated_abundance = (abundance >= 10000) ? 10000 : abundance;
#if OMP
histo_count_omp[tid][saturated_abundance]++;
#else
histo_count[saturated_abundance]++;
#endif
}
if (abundance >= nks && abundance <= max_couv)
{
NbSolid_omp[tid]++;
SolidKmers->write_element_buffered(&previous_kmer,tid);
if (write_count)
SolidKmers->write_buffered(&abundance, sizeof(abundance),tid, false);
}
abundance = 1;
distinct_kmers_per_partition[p]++;
}
previous_kmer = current_kmer;
}
//last kmer
distinct_kmers_per_partition[p]++;
if(output_histo)
{
uint_abundance_t saturated_abundance;
saturated_abundance = (abundance >= 10000) ? 10000 : abundance;
#if OMP
histo_count_omp[tid][saturated_abundance]++;
#else
histo_count[saturated_abundance]++;
#endif
}
if (abundance >= nks && abundance <= max_couv)
{
NbSolid_omp[tid]++;
SolidKmers->write_element_buffered(&previous_kmer,tid);
if (write_count)
SolidKmers->write_buffered(&abundance, sizeof(abundance),tid, false);
}
}
if (verbose >= 1)
fprintf(stderr,"%cPass %d/%d, loaded and sorted partition %d/%d, found %lld solid kmers so far",13,current_pass+1,nb_passes,p+1,nb_partitions,(long long)(NbSolid_omp[tid]));
if (verbose >= 2)
printf("\nPass %d/%d partition %d/%d %ld distinct kmers\n",current_pass+1,nb_passes,p+1,nb_partitions,/*total_kmers_per_partition[p],*/distinct_kmers_per_partition[p]);
#if !SINGLE_BAR
if (verbose == 0 && nb_threads==1)
progress.inc(1);
else if (verbose == 0 && nb_threads>1)
progress.inc(1,tid);
#endif
redundant_partitions_file[p]->close();
remove(redundant_filename[p]);
} // end for partitions
#if OMP
//merge histo
if(output_histo)
{
for (int cc=1; cc<10001; cc++) {
uint64_t sum_omp = 0;
for(int ii=0;ii<nb_threads;ii++)
{
sum_omp += histo_count_omp[ii][cc];
}
histo_count[cc] = sum_omp;
}
}
#endif
#if !SINGLE_BAR
if (verbose == 0 && nb_threads == 1)
progress.finish();
else if (verbose == 0 && nb_threads > 1 )
progress.finish_threaded();
#endif
if (verbose) fprintf(stderr,"\n");
if (verbose >= 2)
{
STOPWALL(debtri,"Reading and sorting partitions");
STOPWALL(debpass,"Pass total");
}
if(use_compressed_reads)
binread->close();
//delete
for (uint32_t p=0;p<nb_partitions;p++)
{
delete redundant_partitions_file[p] ;
}
}
//single bar
#if SINGLE_BAR
if (verbose == 0 && nb_threads == 1)
progress.finish();
else if (verbose == 0 && nb_threads > 1 )
progress.finish_threaded();
#endif
if(output_histo)
{
FILE * histo_file = fopen(return_file_name(histo_file_name),"w");
for (int cc=1; cc<10001; cc++) {
fprintf(histo_file,"%i\t%llu\n",cc,(unsigned long long)(histo_count[cc]));
}
fclose(histo_file);
}
free(histo_count);
NbSolid = NbSolid_omp[0];
#if OMP
NbSolid=0;
for(int ii=0;ii<nb_threads;ii++)
{
NbSolid += NbSolid_omp[ii];
}
#endif
SolidKmers->close();
printf("\nSaved %lld solid kmers\n",(long long)NbSolid);
rmdir(temp_dir);
STOPWALL(count,"Counted kmers");
fprintf(stderr,"\n------------------ Counted kmers and kept those with abundance >=%i, \n",nks);
}
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