Closed:Issues generating bcf file with samtools

Question

[williamsbrian5064]

I am using samtools to make a bcf file but I am having some issues. I am not really sure what is going on here and I was hoping to get some help! To generate my bam file I used trimmomatic, bwa, and picard. I am not too sure what is going on here because none of my other files are giving me any issues.

So the issue I am having here is that when I run the following command, the bcf file that is generated never gets larger over time. It just stays at 0 bytes. I am not sure why this is happening? I had no issues with my other samples.

samtools mpileup --redo-BAQ --min-BQ 30 --per-sample-mF -C 50 --output-tags DP,DV,DPR,INFO/DPR,DP4,SP -u -f Felis_catus.Felis_catus_9.0.dna_sm.toplevel.fa --BCF C04893_L001.sorted.dedup.bam > C04893.bcf

the output from samtools flagstat from the file that is giving me issues

690090027 + 0 in total (QC-passed reads + QC-failed reads)
7861265 + 0 secondary
0 + 0 supplementary
52950324 + 0 duplicates
688355595 + 0 mapped (99.75% : N/A)
682228762 + 0 paired in sequencing
341114381 + 0 read1
341114381 + 0 read2
657843484 + 0 properly paired (96.43% : N/A)
679649948 + 0 with itself and mate mapped
844382 + 0 singletons (0.12% : N/A)
19554958 + 0 with mate mapped to a different chr
16483263 + 0 with mate mapped to a different chr (mapQ>=5)

An example of a file that is working correctly

619420497 + 0 in total (QC-passed reads + QC-failed reads)
8721163 + 0 secondary
0 + 0 supplementary
89789840 + 0 duplicates
617477073 + 0 mapped (99.69% : N/A)
610699334 + 0 paired in sequencing
305349667 + 0 read1
305349667 + 0 read2
577735322 + 0 properly paired (94.60% : N/A)
608184428 + 0 with itself and mate mapped
571482 + 0 singletons (0.09% : N/A)
27685608 + 0 with mate mapped to a different chr
23986111 + 0 with mate mapped to a different chr (mapQ>=5)