ck7/abawaca

abawaca is a binning program for metagenomics

abawaca's Issues

License?

Hello,

Since you did not precise any license, the default copyright laws apply.
Is it intended? Do you plan to make your project open source?

Thank you

Some troubles with abawaca

Hello,
I'm a student in China. And recently I feel great interests in binning. So I have tried different binning methods. However, when I am trying the abawaca method. I have some troubles with it. First, my college has tried the old version of it and he told me the usage. But I am interested in the new version . But the usage is different. It told me to offer the sam-files-glob and source-sam-file. In my opinion, source-sam-file is the raw data mapping to the scaffold data and get the sam file. But I don't know the what sam-file-glob is . Could you please tell me?

A release, or at least a manual?

Hi, are there any plans for an official release of this algorithm? At least a bare-bones manual/readme would be appreciated. I'd really like to use it on my data.

Thanks!

abawaca-build

Hi

Since, the "help" for abawaca does'nt seem to exist, requesting your help with the abawaca-build step. How does one generate the sam glob files?

If I have a depth/coverage profile, generated, say using METABAT, can I use that instead?

Best,
Aditya

File format of .names and .lrn file

ABAWACA requires a .names and .lrn file as input. What information should be contained in these files and what is the expect format?

Usage and Maximum number of dimesions

Hello, could you please provide a more detailed information on the input files? Is there a limit to the number of dimensions that can be used? I have been trying to run ABAWACA with .lrn and .names file formatted exactly like the ESOM input. I am using Kmer content, abundance and coverage of contigs across samples and also taxonomic affiliation (In a total of 3471 data points and ~14700 dimensions). However, I keep getting errors like these if I input a .lrn file with more than 1510 dimensions:

src/ClusterData.cpp (135): Fatal error: number of dimensions found is 1, expected to find 1510: 0991055075714494

Is this some kind of memory issue that causes the input files not to be read correctly? I already checked the files in several ways to make sure all dimensions are actually there, with numeric values, and unique names.

Any help is much appreciated.

stack smashing error

Hi there, I am getting the following error while trying to run abawaca:

*** stack smashing detected ***: abawaca terminated
======= Backtrace: =========
/lib64/libc.so.6(__fortify_fail+0x37)[0x7f99fdd5ed87]
/lib64/libc.so.6(__fortify_fail+0x0)[0x7f99fdd5ed50]
abawaca(+0x65f4)[0x55f2547ae5f4]
abawaca(+0x3986)[0x55f2547ab986]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f99fdc70c05]
abawaca(+0x5c89)[0x55f2547adc89]
======= Memory map: ========
55f2547a8000-55f2547ab000 r--p 00000000 00:29 30485605303 /home/clb21565/miniconda3/envs/abawaca/bin/abawaca
55f2547ab000-55f2547b5000 r-xp 00003000 00:29 30485605303 /home/clb21565/miniconda3/envs/abawaca/bin/abawaca
55f2547b5000-55f2547b8000 r--p 0000d000 00:29 30485605303 /home/clb21565/miniconda3/envs/abawaca/bin/abawaca
55f2547b8000-55f2547b9000 r--p 0000f000 00:29 30485605303 /home/clb21565/miniconda3/envs/abawaca/bin/abawaca
55f2547b9000-55f2547ba000 rw-p 00010000 00:29 30485605303 /home/clb21565/miniconda3/envs/abawaca/bin/abawaca
55f2550bc000-55fa6dce9000 rw-p 00000000 00:00 0 [heap]

Job ID: 920593
Cluster: dragonstooth
User/Group: clb21565/clb21565
State: FAILED (exit code 134)
Nodes: 1
Cores per node: 24
CPU Utilized: 00:18:33
CPU Efficiency: 4.16% of 07:26:24 core-walltime
Job Wall-clock time: 00:18:36
Memory Utilized: 38.47 GB
Memory Efficiency: 19.24% of 200.00 GB