Closed duanshumeng closed 1 year ago
Hi @duanshumeng,
Hard to help with so little information, please provide the exact line of code that you have used so I can have a little bit of context. Is your BAM indexed? Can you check that you provide the absolute path? Can you check it's not truncated? Can you run (in a bash terminal, not par of ASCAT) alleleCounter without any error (alleleCounter -l myloci.txt -b myBAM.bam -o test.out -m 20 -q 35 -d
)? It seems like there is a problem with the BAM or with the alleleCounter configuration here.
Cheers,
Tom.
Hi @duanshumeng,
Hard to help with so little information, please provide the exact line of code that you have used so I can have a little bit of context. Is your BAM indexed? Can you check that you provide the absolute path? Can you check it's not truncated? Can you run (in a bash terminal, not par of ASCAT) alleleCounter without any error (
alleleCounter -l myloci.txt -b myBAM.bam -o test.out -m 20 -q 35 -d
)? It seems like there is a problem with the BAM or with the alleleCounter configuration here.Cheers,
Tom.
Thank you for you reply. I followed your guide and run "alleleCounter -l myloci.txt -b myBAM.bam -o test.out -m 20 -q 35 -d" ,and there were new errors, and I don't understand. The command and error: root@9def351600c8:/home/ASCAT/WGS# ~/miniconda3/envs/hrd/bin/alleleCounter -l GC_G1000_hg38.txt -b ../demo_bam/Test_1_N.dedup.bam -o test.out -m 20 -q 35 -d Reading locis [ERROR] (./src/alleleCounter.c: get_position_info_from_file:288 errno: No such file or directory) Error parsing loci file line number 0 as a string match: ' Chr Position 25bp 50bp 100bp 200bp 500bp 1kb 2kb 5kb 10kb 20kb 50kb 100kb 200kb 500kb 1Mb '. [ERROR] (./src/alleleCounter.c: read_locis_from_file:359 errno: None) Error trying to fetch position from file at line 0. Done reading locis [ERROR] (./src/alleleCounter.c: main:411 errno: None) Error reading loci_stats from file. munmap_chunk(): invalid pointer Aborted (core dumped) root@9def351600c8:/home/ASCAT/WGS# less GC_G1000_hg38.txt
Hi @duanshumeng,
It seems like there is some confusion about the input files. In your code, you are using the GC correction file (GC_G1000_hg38.txt
) as the loci file for alleleCounter, these are two different sets of files. Can you give it a try with the correct loci files (here for WGS data)?
Cheers,
Tom.
Hi @duanshumeng,
It seems like there is some confusion about the input files. In your code, you are using the GC correction file (
GC_G1000_hg38.txt
) as the loci file for alleleCounter, these are two different sets of files. Can you give it a try with the correct loci files (here for WGS data)?Cheers,
Tom.
Thank you , I solved this problem as your your advice. But there is new error occurs, that is:
ascat.prepareHTS(
- tumourseqfile = tumor_bam,
- normalseqfile = normal_bam,
- tumourname = tumor_name,
- normalname = normal_name,
- allelecounter_exe = allelecounter,
- alleles.prefix = alleles_prefix,
- loci.prefix = loci_prefix,
- gender = gender,
- genomeVersion = hg_version,
- nthreads = 40,
- tumourLogR_file = paste0(tumor_name, "_LogR.txt"),
- tumourBAF_file = paste0(tumor_name, "_BAF.txt"),
- normalLogR_file = paste0(normal_name, "_LogR.txt"),
- normalBAF_file = paste0(normal_name, "_BAF.txt"),
- BED_file = bed_file) Error in readAlleleCountFiles(tumourAlleleCountsFile.prefix, ".txt", chrom_names, : length(files) > 0 is not TRUE
Can you have a look into the files called *_alleleFrequencies_chr*
and show a few lines here?
Can you have a look into the files called
*_alleleFrequencies_chr*
and show a few lines here?
Sorry, files called *_alleleFrequencies_chr*
don't exist. Is there something wrong?
Yes, something is clearly wrong. Such files should be generated early on when running ascat.prepareHTS
(https://github.com/VanLoo-lab/ascat/blob/master/ASCAT/R/ascat.prepareHTS.R lines 261 & 273). Something is wrong in your configuration but, again, I have too little information to assist you at this point.
Hi, pardon me for jumping into the conversation but I am facing the same issue -
Error in readAllelesFiles(alleles.prefix, ".txt", chrom_names) :
length(files) > 0 is not TRUE
and I have generated _alleleFrequencies_chr files, here are some of the lines -
head PATAAK_Day0_alleleFrequencies_chr*.txt
==> PATAAK_Day0_alleleFrequencies_chr1.txt <==
#CHR POS Count_A Count_C Count_G Count_T Good_depth
chr1 16103 0 0 1 13 14
chr1 51479 0 0 0 14 14
chr1 51898 0 32 0 0 32
chr1 51928 0 0 29 0 29
chr1 54490 0 0 33 0 33
chr1 54708 0 5 27 0 32
chr1 54716 0 22 0 2 24
chr1 54753 0 0 10 30 40
chr1 55299 0 15 0 17 32
==> PATAAK_Day0_alleleFrequencies_chr10.txt <==
#CHR POS Count_A Count_C Count_G Count_T Good_depth
chr10 11501 4 25 0 0 29
chr10 36097 0 0 9 0 9
chr10 47317 0 0 17 0 17
chr10 47347 0 24 0 0 24
chr10 47460 25 0 0 0 25
chr10 47754 0 4 0 21 25
chr10 47792 27 0 0 0 27
chr10 47804 0 0 0 26 26
chr10 47876 0 5 0 20 25
==> PATAAK_Day0_alleleFrequencies_chr11.txt <==
#CHR POS Count_A Count_C Count_G Count_T Good_depth
chr11 115634 0 0 0 0 0
chr11 128425 0 1 0 0 1
chr11 128429 0 1 0 0 1
chr11 128446 0 0 1 0 1
chr11 128557 0 0 0 0 0
chr11 128770 0 0 0 0 0
chr11 146846 0 0 0 0 0
chr11 157501 0 0 0 0 0
chr11 159344 0 0 0 0 0
Is anything wrong with these?
Hi @abhijitcbio,
Please provide the exact line of code that you have used so I can have a little bit of context. Your *_alleleFrequencies_chr*
files look good but your issue is related to the allele files (readAllelesFiles
). I need to know what is the value of alleles.prefix
when you run ascat.prepareHTS
, if such files look good and if they can be accessed from where you run ASCAT.
Cheers,
Tom.
Here it is
ascat.prepareHTS(
tumourseqfile = "../BAM_input_for_SV_callers/PATAAK_Day0_marked_duplicates.MAPQ20.bam",
normalseqfile = "../BAM_input_for_SV_callers/PATAAK_Day28_marked_duplicates.MAPQ20.bam",
tumourname = "PATAAK_Day0",
normalname = "PATAAK_Day28",
allelecounter_exe = "~/perl5/bin/alleleCounter",
alleles.prefix = " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr",
loci.prefix = "../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_loci_chr",
gender = "XX",
genomeVersion = "hg38",
nthreads = 8,
tumourLogR_file = "PATAAK_Day0_LogR.txt",
tumourBAF_file = "PATAAK_Day0_BAF.txt",
normalLogR_file = "PATAAK_Day28_LogR.txt",
normalBAF_file = "PATAAK_Day28_BAF.txt")
I also tested with that particular portion of the code and tried to print the files by modifying the codes like this
readAllelesFiles=function(prefix,suffix,chrom_names,add_chr_string=F) {
files=paste0(prefix,chrom_names,suffix)
print (files) #print the file names, stage1
print ("_____") #print a demarcation
files=files[sapply(files,function(x) file.exists(x) && file.info(x)$size>0)]
print (files) #print against stage2
print (length(files)) #print the length
stopifnot(length(files)>0)
print (files)
data=do.call(rbind,lapply(files,function(x) {
tmp=data.frame(data.table::fread(x,sep='\t',showProgress=F,header=T))
tmp=tmp[!is.na(tmp[,2] & !is.na(tmp[,3])),]
tmp=tmp[!duplicated(tmp[,1]),]
tmp$chromosome=gsub(paste0(prefix,'(',paste(chrom_names,collapse='|'),')',suffix),'\\1',x)
if (add_chr_string) tmp$chromosome=paste0('chr',tmp$chromosome)
tmp=tmp[,c(4,1:3)]
rownames(tmp)=paste0(tmp[,1],'_',tmp[,2])
return(tmp)
}))
stopifnot(nrow(data)>0)
return(data)
}
and this generated the following
Reading locis
Done reading locis
Multi pos start:
[1] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt"
[2] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr2.txt"
[3] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr3.txt"
[4] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr4.txt"
[5] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr5.txt"
[6] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr6.txt"
[7] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr7.txt"
[8] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr8.txt"
[9] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr9.txt"
[10] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr10.txt"
[11] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr11.txt"
[12] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr12.txt"
[13] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr13.txt"
[14] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr14.txt"
[15] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr15.txt"
[16] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr16.txt"
[17] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr17.txt"
[18] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr18.txt"
[19] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr19.txt"
[20] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr20.txt"
[21] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr21.txt"
[22] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr22.txt"
[23] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chrX.txt"
[1] "____"
character(0)
[1] 0
Error in readAllelesFiles(alleles.prefix, ".txt", chrom_names) :
length(files) > 0 is not TRUE
Calls: Test.ascat.prepareHTS ... ascat.getBAFsAndLogRs -> readAllelesFiles -> stopifnot
Execution halted
So, it is showing the files at stage1 but not at stage2. The files are accessible from the same folder.
ls ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr*
../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr15.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr20.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr5.txt
../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr10.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr16.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr21.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr6.txt
../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr11.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr17.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr22.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr7.txt
../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr12.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr18.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr23.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr8.txt
../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr13.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr19.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr3.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr9.txt
../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr14.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr2.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr4.txt ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chrX.txt
Thanks for your help.
Hi @abhijitcbio,
Thanks for providing such a detailed report. That's really weird, could you split the file.exists(x) && file.info(x)$size>0)
instruction so we can see if the files aren't considered because there is an issue with file.exists(x)
or file.info(x)$size
? Can you also double-check that you don't usesetwd
in your script (so you are located in the right folder) and head 1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt
to make sure that the files aren't empty? This can be checked in your modified function where you can:
print(getwd())
print(file.exists('../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt'))
print(file.info('../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt')$size)
print(head(readLines('../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt')))
Cheers,
Tom.
Here is the modified code
readAllelesFiles=function(prefix,suffix,chrom_names,add_chr_string=F) {
files=paste0(prefix,chrom_names,suffix)
print (files)
print ("____")
print (getwd())
print (files[1])
print (file.exists(files[1]))
print (file.info(files[1])$size)
print (head(readLines(files[1])))
print ("____")
files=files[sapply(files,function(x) file.exists(x) && file.info(x)$size>0)]
print (files)
print (length(files))
stopifnot(length(files)>0)
print (files)
data=do.call(rbind,lapply(files,function(x) {
tmp=data.frame(data.table::fread(x,sep='\t',showProgress=F,header=T))
tmp=tmp[!is.na(tmp[,2] & !is.na(tmp[,3])),]
tmp=tmp[!duplicated(tmp[,1]),]
tmp$chromosome=gsub(paste0(prefix,'(',paste(chrom_names,collapse='|'),')',suffix),'\\1',x)
if (add_chr_string) tmp$chromosome=paste0('chr',tmp$chromosome)
tmp=tmp[,c(4,1:3)]
rownames(tmp)=paste0(tmp[,1],'_',tmp[,2])
return(tmp)
}))
stopifnot(nrow(data)>0)
return(data)
}
And here is the outcome
Multi pos start:
[1] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt"
[2] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr2.txt"
[3] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr3.txt"
....
[1] "____"
[1] "/mnt/bioadhoc-temp/Groups/abhijit/overflow/proj_overflow/Porject/Analysis/WGS/ASCAT/result"
[1] " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt"
[1] FALSE
[1] NA
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'head': cannot open the connection
Calls: Test.ascat.prepareHTS ... head -> readLines -> file -> .handleSimpleError -> h
In addition: Warning message:
In file(con, "r") :
cannot open file ' ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt': No such file or directory
Execution halted
(base) pwd
/mnt/bioadhoc-temp/Groups/abhijit/overflow/proj_overflow/Porject/Analysis/WGS/ASCAT/result
(base) ls -trl ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt
-rwxrwxr-x+ 1 abhijit domain_users 28853842 Jul 1 2020 ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt
Somehow, it can't access the files and here's few lines from the index file
(base) head ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr1.txt
position a0 a1
16103 4 3
51479 4 1
51898 2 1
51928 3 1
54490 3 1
54708 3 2
54716 2 4
54753 4 3
55299 2 4
Hi @abhijitcbio,
I can't think of a reason why this doesn't work, it seems like the file is at the expected location but R can't access it for some reason. How about providing the absolute path instead? Should be: alleles.prefix = "/mnt/bioadhoc-temp/Groups/abhijit/overflow/proj_overflow/Porject/Analysis/WGS/ASCAT/1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr"
You can also use skip_allele_counting_tumour=T, skip_allele_counting_normal=T
since you have generated the allele counts for this sample already.
Cheers,
Tom.
If providing the absolute path doesn't help, then the ultimate check would be to make sure that you can access your files from where you are, outside of the ASCAT environment. Like if you consider using alleles.prefix = " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr"
, then, right before running ASCAT, try something like:
alleles.prefix = " ../1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_allele_index_chr"
alleleFiles=paste0(alleles.prefix,c(1:22,'X'),'.txt')
print(getwd())
print(alleleFiles)
print(file.exists(alleleFiles))
If this doesn't work, then it would point to an issue with your environment rather than an issue with ASCAT.
Cheers,
Tom.
Hi @duanshumeng,
I still don't have any information about your problem. You did provide the following piece of code:
ascat.prepareHTS(
tumourseqfile = tumor_bam,
normalseqfile = normal_bam,
tumourname = tumor_name,
normalname = normal_name,
allelecounter_exe = allelecounter,
alleles.prefix = alleles_prefix,
loci.prefix = loci_prefix,
gender = gender,
genomeVersion = hg_version,
nthreads = 40,
tumourLogR_file = paste0(tumor_name, "_LogR.txt"),
tumourBAF_file = paste0(tumor_name, "_BAF.txt"),
normalLogR_file = paste0(normal_name, "_LogR.txt"),
normalBAF_file = paste0(normal_name, "_BAF.txt"),
BED_file = bed_file)
But I still don't know what tumor_bam
is, what alleles_prefix
is, what loci_prefix
is what log messages are, is there is any extra step before, etc. I can't help if I only have sparse information.
Cheers,
Tom.
Hi,
providing the absolute path solved the issue. Thanks a lot for the help.
ascat version 3.0.0
Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. munmap_chunk(): invalid pointer munmap_chunk(): invalid pointer Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. munmap_chunk(): invalid pointer Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. Done reading locis Multi pos start: munmap_chunk(): invalid pointer Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. Done reading locis Multi pos start: Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. Done reading locis Multi pos start: Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. munmap_chunk(): invalid pointer [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) wDone reading locis Multi pos start: hen trying to iterate through region. munmap_chunk(): invalid pointer [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. munmap_chunk(): invalid pointer [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. munmap_chunk(): invalid pointer munmap_chunk(): invalid pointer Done reading locis Multi pos start: munmap_chunk(): invalid pointer Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. munmap_chunk(): invalid pointer Aborted Aborted munmap_chunk(): invalid pointer munmap_chunk(): invalid pointer Aborted Aborted Aborted Done reading locis Multi pos start: Aborted munmap_chunk(): invalid pointer munmap_chunk(): invalid pointer Done reading locis Multi pos start: [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. [E::sam_itr_next] Null iterator [ERROR] (src/bam_access.c: bam_access_get_multi_position_base_counts:379 errno: No such file or directory) Error detected (-2) when trying to iterate through region. [ERROR] (./src/alleleCounter.c: main:432 errno: None) Error scanning through bam file for loci list with dense snps. Aborted Aborted