warning during make plus no output file

[jervdberg]

Hi!

I was installing BAFextract, which seemed to work until I got these warning messages during the install

g++ -c -Wall -O3 src/main.cpp -o src/main.o
src/main.cpp: In function 'void dump_nucleotide_pileup_per_SAM_file(char*, std::vector<char*>, std::vector, char*, int, int, int&)':
src/main.cpp:595:144: warning: format '%d' expects a matching 'int' argument [-Wformat=]
fprintf(stderr, "Loaded pileup is not the same length as the chromosome info: %s: %d, %d\n", chr_ids->at(i_chr), chr_lengths->at(i_chr));
^
src/main.cpp: In function 'int main(int, char**)':
src/main.cpp:1062:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i_chr = 0; i_chr < chr_ids->size(); i_chr++)
^
src/main.cpp:1098:64: warning: array subscript has type 'char' [-Wchar-subscripts]
bool is_alternate_allele = (nuc_2_num_array[cur_chr_seq[i]] != i_all);
^
g++ -c -Wall -O3 src/utils.cpp -o src/utils.o
g++ -c -Wall -O3 src/ansi_string.cpp -o src/ansi_string.o
src/ansi_string.cpp: In static member function 'static std::vector<char*>* t_string::copy_tokens_2_strs(t_string_tokens*)':
src/ansi_string.cpp:1367:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i_t = 0; i_t < toks->size(); i_t++)
^
g++ -c -Wall -O3 src/genomics_coords.cpp -o src/genomics_coords.o
g++ -O3 -o bin/BAFExtract src/main.o src/utils.o src/ansi_string.o src/genomics_coords.

When I run this code, on a sorted 10X cellranger generated BAMfile

samtools view ./bam_input/possorted_genome_bam.bam | ./BAFExtract -generate_compressed_pileup_per_SAM stdin hg38.list ./bam_input/ 50 0; ./BAFExtract -get_SNVs_per_pileup hg38.list ./bam_input/ ./genome_fasta_pileup_dir/ 20 4 0.1 FB016.snps

I do get a *.snps output but it is empty and very small. I also tried tweaking the filter option such as the 20 reads per SNP position and the 4 reads supporting the SNP. However, this did not change the output

I would be really gratefull if you could help me out!

kind regards,

Jeroen van den Berg

[akdess]

Hi Jeroen,

It is weird that the output is very small. If possible can you send us the bam file so we can have a more detailed look on it? You can also send a portion of the bam file. email akdess at gmail com

Thanks a lot,
Akdes

[avln24]

Hi there!

I am also trying to use BAFExtract to generate baf files for use with CaSpER. I am trying to run BAFExtract on a 10x Cell Ranger generated BAM file. When I try to apply BAFExtract to the BAM file, the output file I get is empty and very small.

I was wondering if you found the solution to this problem?

Thank you

[yangmeili1]

I got the same problem, got a empty snp file. Have you solved this problem? Do you have any suggestions? thanks a lot !

[avln24]

I haven't solved the problem and am waiting for a response, were you able to solve it?

[arjun0502]

@avln24 @yangmeili1 @jervdberg @akdess Did you figure out this issue? I also ran BAFExtract on a 10x Cell Ranger generated BAM file and got an empty output snp file.....

[LordSushiPhoenix]

I have a similar problem on two different systems.

On a linux system I get compile time warnings, similar to the original report here, but then the program seems to run fine until it spits out a blank baf signal. I've attached the output of running make clean; make and then calling BAFextract as outlined in the tutorial.
bafextract_compile_run_linux.txt

This system is running g++ 9.3.0 and linux 3.10.0 on a compute canada cluster.

On my Intel Macbook pro, running macOS 11.5.2 with Apple clang 12.0.5 I get a different warning at compile time, but similar behaviour at run time.
bafextract_compile_run_mac.txt

Both systems output an empty file after running for a few hours. The input dataset is from 10x chromium. Please let me know if there is any other information I can provide to help solve the issue.