Question about error

[Former user]

Hello MetaBAT team,

I have an issue running metabat2 to bin my contigs with coverage file from anvi'o as shown below. Unlike error message said, number of columns in coverage files is not uneven. Could you help me to fix this issue?

#GR-merged_splits (base) -bash-4.2$ metabat2 -i GR-merged-CONTIGS.fa -a GR-merged-COVs.txt -o bins_dir/bin -v -d -m 1500 -t 15 MetaBAT 2 (2.15 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=1585893863 [00:00:00] Executing with 15 threads [00:00:00] Parsing abundance file [Error!] Number of columns (excluding the first column) in abundance data file is not even.

#GR-merged-contigs (base) -bash-4.2$ metabat2 -i GR-merged-CONTIGS.fa -a GR-merged-COVs.txt -o bins_dir/bin -v -d -m 1500 -t 15 MetaBAT 2 (2.15 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=1585893731 [00:00:00] Executing with 15 threads [00:00:00] Parsing abundance file [Error!] Number of columns (excluding the first column) in abundance data file is not even. (base) -bash-4.2$

#GR-merged_splits_Q2Q3 (base) -bash-4.2$ metabat2 -i GR-merged-CONTIGS.fa -a GR-merged-COVs.txt -o bins_dir/bin -v -d -m 1500 -t 15 MetaBAT 2 (2.15 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=1585893919 [00:00:00] Executing with 15 threads [00:00:00] Parsing abundance file [Error!] Number of columns (excluding the first column) in abundance data file is not even.

#GR-merged-contigs_Q2Q3 (base) -bash-4.2$ metabat2 -i GR-merged-CONTIGS.fa -a GR-merged-COVs.txt -o bins_dir/bin -v -d -m 1500 -t 15 MetaBAT 2 (2.15 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=1585893811 [00:00:00] Executing with 15 threads [00:00:00] Parsing abundance file [Error!] Number of columns (excluding the first column) in abundance data file is not even.

[Rob Egan]

MetaBAT is currently not compatible with the coverage files that come out of anvi’o and at the moment we do not have plans to adapt it. The metabat workflow requires coverages generated from the mapping of the reads to the assembly and this is required this for several reasons. Because some read mapping software is more aggressive than others, metabat reads the quality of the mapping and chooses what portion if any to include as counted coverage. This is critical for performing well for resolving bins at the strain level. Additionally the standard deviation of a scaffold’s coverage is important to the calculations.

Please get or generate the BAM files of the reads to the assembly for proper usage of MetaBAT

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