Hi:
I am writing to know users experience about mpileup snp calling with human whole genome bam file.
my 'de-duped' sorted bam file is ~55GB in size.
When I ran mpileup on these files, it has been running continuously for 4 days on a cluster node with 16 processor 64gb node.
For some bam files:
the output file of the node job has this following information:
[bcfview] 26800000 sites processed.
[afs] 0:91696.193 1:4741.654 2:3562.153
[bcfview] 26900000 sites processed.
[afs] 0:89785.449 1:6797.768 2:3416.783
Similarly the error output file has this information:
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
Terminated
I have two questions in this context:
1. Is my process complete or this is a genuine error that mpileup is not finished.
2. What is the better practice of calling SNPs using mpileup for human whole genome sequence data (where a bam file is over 50GB in size - if size is a concern).
Thanks
Adrian
I am writing to know users experience about mpileup snp calling with human whole genome bam file.
my 'de-duped' sorted bam file is ~55GB in size.
When I ran mpileup on these files, it has been running continuously for 4 days on a cluster node with 16 processor 64gb node.
For some bam files:
the output file of the node job has this following information:
[bcfview] 26800000 sites processed.
[afs] 0:91696.193 1:4741.654 2:3562.153
[bcfview] 26900000 sites processed.
[afs] 0:89785.449 1:6797.768 2:3416.783
Similarly the error output file has this information:
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
Terminated
I have two questions in this context:
1. Is my process complete or this is a genuine error that mpileup is not finished.
2. What is the better practice of calling SNPs using mpileup for human whole genome sequence data (where a bam file is over 50GB in size - if size is a concern).
Thanks
Adrian
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