no error but result file is empty

[AmberFu]

Hi @wanpinglee

I download some BAM files which mapped to the GRCh38 standard set.
So, I first process this standard FASTA with Jellyfish:

$ jellyfish bc -m 25 -s 3G -t 8 -o Homo_sapiens_assembly38.bc Homo_sapiens_assembly38.fasta
$ jellyfish count -m 25 -s 1G -t 8 -o Homo_sapiens_assembly38.jf --bc Homo_sapiens_assembly38.bc Homo_sapiens_assembly38.fasta
// output file size
$ ls -lh
total 9.1G
-rw-------. 1 fup compute-jin810 7.9G Aug 13 23:51 Homo_sapiens_assembly38.bc
-rw-------. 1 fup compute-jin810 1.3G Aug 14 00:23 Homo_sapiens_assembly38.jf

Then, ​I ran JAX-CNV GrabJellyfishKmer​:​ (using Docker wanpinglee/jax-cnv:latest)

$ /tools/JAX-CNV/bin-linux/JAX-CNV GrabJellyfishKmer --ascii ​\
​-i Homo_sapiens_assembly38.jf ​\
​-f Homo_sapiens_assembly38.fasta ​\
​-o Homo_sapiens_assembly38.kmer
 
 ​// output file size:​
-rw-r--r--. 1 fup domain users   3.0G Aug 14 02:45 ​​Homo_sapiens_assembly38.kmer
-rw-------. 1 fup compute-jin810  727 Aug 14 01:53 Homo_sapiens_assembly38.kmer.fai

​In this step, my output .fai file were ​interrupt without any error.
So, I index the Homo_sapiens_assembly38.kmer with samtools to get validate fai file.

​$ samtools faidx Homo_sapiens_assembly38.kmer --fai-idx Homo_sapiens_assembly38.kmer.fai​

​Finally, I ran JAX-CNV GetCnvSignal: (using Docker wanpinglee/jax-cnv:latest)
​

​$ /tools/JAX-CNV/bin-linux/JAX-CNV GetCnvSignal \
-f Homo_sapiens_assembly38.fasta \
-k Homo_sapiens_assembly38.kmer \
-b BAMs/UDN369194-861-05ac424d-0a44-46fe-b6f6-0fcfe0788d2a.bam \
-o jax_cnv_GetCnvSignal_on_UDN369194.result \
--log JAX_CNV_GetCnvSignal_on_UDN369194.log 
Gender: Cannot determine. 
Message: The estimated coverage is -2147483648 
Message: Processing chr1:0-248956421 
Message: Loading chromosome chr1 is done. 
Message: Loading kmer of chromosome chr1 is done.​
​...
Message: Loading chromosome HLA-DRB1*16:02:01 is done.
Message: Loading kmer of chromosome HLA-DRB1*16:02:01 is done.
Message: HMM completes.
1 HLA-DQA1*01:01:02 49 5548 5500
1 HLA-DQA1*01:02:01:01 49 6348 6300
...
1 HLA-DRB1*16:02:01 49 9898 9850
Filter checking for HLA-DQA1*01:01:02 49 5500 
Message: Loading kmer of chromosome HLA-DQA1*01:01:02 is done. 
0 0.0118182 
1 0 
2 0 
3 0.00636364 
4 0 
5 0 
6 0 
7 0 
8 0 
9 0
 0 10 10 0 
Filter 
... 
Filter checking for chr1 10049 125174600 
Message: Loading kmer of chromosome chr1 is done. 
0 0.0306559 
1 0.029093 
2 0.0187111 
3 0.0145986 
4 0.0127288 
5 0.0127871 
6 0.0203479 
7 0.0137128 
8 0.0194234 
9 0.0534288 
0 10 10 0 
Filter​
​...


// OUTPUT:
-rw-------. 1 fup compute-jin810 2.7G Aug 15 01:15 JAX_CNV_GetCnvSignal_on_UDN369194.log 
-rw-------. 1 fup compute-jin810 0 Aug 15 01:12 jax_cnv_GetCnvSignal_on_UDN369194.result​

​I tried 5 different BAMs, and all ​of them had no result. (result file is empty)

And, I'm wondering that the logs shows:

Gender: Cannot determine. 
Message: The estimated coverage is -2147483648 

Why is our BAM file had a huge negative coverage?
And do you have any suggestion for fix this problem? Thank!