Estimating the curve with low read count

[JeffreyMaurer]

Hi there.

I'm trying to run preseq 3.1.1 on a new Ubuntu 20.04.1 system through the command line. I have a prepared bam file, but when I run the program, I encounter this:

$ preseq lc_extrap PC1-PT.bam -B -P -e 2.1e9 -s 1e8 -seg_len 1000000000 -o PC1.preseq
ERROR:  max count before zero is less than min required count (4) duplicates removed

Scouring the web for a solution, I look for a solution only to be met with an explanation here. But that doesn't appear accurate. It runs when I use a sam file as input of the same data.

I checked the help section and tried the -D option expecting some quality checks to be bypassed, but alas. Here I am. I want to know if there is any way to bypass this? I did not have this issue when working with version 2.0.3.

As an aside, and I can log this with another issue if it's a large task, one other item I noticed is that all the help pages seem to be formatted incorrectly, even the command line help. When I submit with the input file at the end of the options:

$ preseq lc_extrap  -B -P -e 2.1e9 -s 1e8 -seg_len 1000000000 -o PC1.preseq PC1-PT.bam
ERROR:  problem opening file: -B

I also did not encounter this issue in version 2.0.3.

Thanks.

[terencewtli]

Hi,

I ran both of the commands you listed with the .bam file in the data directory and it runs fine. Would it be possible for you to share your file with me so I can run some tests with it? Either way, these are some strange errors - for the first issue, I just want to confirm that you configured with the --enable-hts option? And for the second error, it looks like the flags are parsed incorrectly, but once again on my end, running the same command runs fine for me.

[andrewdavidsmith]

It seems there is no response after @terencewtli 's answer, so I'll close this and it can be reopened if needed.