Samtools mpileup [E::hts_open_format] Failed to open file .bam

[alnam3]

Are you using the latest version of samtools and HTSlib? If not, please specify.

(run samtools --version)
Yes

Please describe your environment.

• OS (run uname -sr on Linux/Mac OS or wmic os get Caption, Version on Windows)
  Linux 5.3.0-46-generic
• machine architecture (run uname -m on Linux/Mac OS or wmic os get OSArchitecture on Windows)
  x86_64
• compiler (run gcc --version or clang --version)
  7.5.0

Please specify the steps taken to generate the issue, the command you are running and the relevant output.

I'm mapping sequences and then doing SNP calling, using the following steps:

minimap2 -ax map-ont ref.fas mydata.fq | samtools view -b | samtools sort - > outfile.sam 
samtools mpileup -q 10 -aa -d 8000 -uf refs.fas outfile.sam | bcftools call -m > outfile.vcf

And get the error:

[E::hts_open_format] Failed to open file outfile.bam
[mpileup] failed to open outfile.bam : No such file or directory
Failed to read from standard input: unknown file type

I checked, my bam file is in the right folder and I can read it with samtools view.
I recently updated to samtools1.10, so I thought this might be the problem, but checked with an older version (samtools1.7) on files that used to work and it isn't working anymore. What can have happened?
And I know the u option is deprecated but bcftools mpileup gave me a similar error.

Thanks a lot!

[valeriuo]

minimap2 -ax map-ont ref.fas mydata.fq | samtools view -b | samtools sort - > outfile.sam

It seems you are naming your file outfile.sam. Try to rename it to outfile.bam and run the second command again.

[alnam3]

Oops sorry it was a typo in the issue, there was no file name problems in my command line!
(I edited the issue for clarity!)

[alnam3]

It seems I found the problem thanks to this: http://seqanswers.com/forums/archive/index.php/t-4280.html
It was my mistake: I had installed the latest version and then moved the executable in /usr/bin instead of exporting the path /usr/bin/samtools-1.10/ to my path.
I changed that, now it works.

Thanks for your quick reply, and sorry for this quite stupid mistake!