bwa mem - expected runtime?

Question

[truebeliever24]

Hi everyone,

I am running an alignment to the Anna's Hummingbird reeference genome using files of 10 runs that range from 7.6 to 10.2 Gb in size, and 2.2-2.9 giga bases in length.

I am using the command bwa mem -t 24, running on a cluster, using 24 cpus and 12 gb of memory per cpu (the max I could request for the job).

How long should I expect this to take? I've read across different forums of people generating a sam file every few minutes to every few hours or so, but I haven't generated a single sam file and it has been nearly 24 hours. It seems to be stuck on a specific step "M::process read 16790 sequences (240019667 bp)... and I'm not at all sure why.

Thanks for your input!

[h.mon]

Are you piping to samtools, or outputting directly to a sam file? What is you exact command? Are the reads files located at a NFS share?

Side note: I would think (depending on drive speed characteristics) beyond 6-10 cpus is pointless, as probably the limiting factor would be disk IO.

[truebeliever24]

The read files are on the cluster server-as far as I know, I am not using an NFS share. I'm running the following (so I don't think I'm piping to samtools-I am outputting a sam file directly):

bwa mem -t 24 $ref $i.fastqsanger > $i.sam
done

then I plan to run the following:

# SAM to BAM, with read group information
for i in {21..30}; do
    picard AddOrReplaceReadGroups \
                I=$i.sam \
                O=$i.bam \
                RGID=4 \
                RGLB=lib1 \
                RGPL=pacbio \
                RGPU=unit1 \
                RGSM=anna
done

for i in {21..30}; do
        samtools sort $i.bam -o $i.sort.bam
    samtools index $i.sort.bam
done

# Samtools Merge
samtools merge all_runs.bam *.sort.bam

# Mpileup
bcftools mpileup -Ou -f $ref \

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.