Cannot find the contig in abundance file from the assembly file

[Former user]

Hello,

I keep obtaining the error "Cannot find the contig in abundance file from the assembly file" when I run metabat. I generated the abundance file using the "jgi_summarize_bam_contig_depths" command and the file looks fine. From a manual check I can see that the names between the abundance and assembly files are indeed the same. If you could please let me know what might be going on it would be much appreciated.

Thanks.

I noticed that a similar issue was posted on 2015-10-12 but do not see a solution posted.

[Don Kang]

Can you send me your assembly file and the exact command line you used? Thanks.

[Christopher Lawson]

Hi Don,

The assembly and depth files can be found here.

The command I ran was:

metabat -i Co-assembly.fa -a depth.txt -o bin -v

Thanks.

[Don Kang]

Hi Christopher,

The error occurred due to the unexpected new line character ('\r'). Now it is fixed. Please download the latest dev version.

Thanks.

[Christopher Lawson]

I attempted to compile the latest dev code, but it appears that the install script has errors where it is looking for header files. Could you please try compiling using your instructions and see if it's working?

it's seems to be telling the compiler to look in $HOME/samtools/include/bam, but that directory is empty -- a lot of the files it is looking for can manually be found in $HOME/samtools (sam.h and bam.h for example).

[Don Kang]

Was it for OSX? Take a look at those os specific installation instructions. Samtools should be compiled automatically after downloaded. Anyways, for your convenience, I've uploaded binary versions.

[Christopher Lawson]

Hi Don,

we installed the new binaries and everything seems to be working fine. Thanks!