BamM make keeps printing the help message

[mdehollander]

I am trying to create bam files with this command:

bamm make -d spades/contigs.fasta -c sickle/C1_R1.fastq sickle/C1_R2.fastq -t 40

But it keeps printing the help message. According to the help output I have to use at least one of the -c -i and -s options, isn't it. Any hints for the correct command are welcome

[wwood]

Hi,

Thanks for your interest in bamm. In the (longish) help message that is displayed, is there an error printed at the top, e.g.

$ bamm make -d some
********************************************************************************

ERROR:

Specified database (some) is not a valid file

********************************************************************************
... (snip)

[mdehollander]

Thanks for the hint of the long help message. The error message was hidden on my screen. When I output stderr to stdout it became visible. The problem was that the indexes where already present. It is fixed by adding the -K flag to the command.

bamm make -d spades/contigs.fasta -c sickle/C1_R1.fastq sickle/C1_R2.fastq -t 40 2>&1 
********************************************************************************

ERROR:

You didn't specify that index files have been kept but there appears to be bwa index files present.
I'm cowardly refusing to run so as not to risk overwriting.
Force overwriting to create new indices

********************************************************************************

usage: bamm make -d DATABASE [-i INTERLEAVED [INTERLEAVED ...]]

Thanks!

[wwood]

Unless Mike objects too strongly, the output in the next version will now be shorter so it doesn't run off your screen.