WARNING: bam has improper refpos vs reflen:

[huizhen yan]

This is my code:

time runMetaBat.sh --maxP 95 --minS 60 --maxEdges 500 -m 2000 -t 0 contig.fa S4R1.sort.bam

I did assemble using IDBA-UD, and sort with samtools.

I got an error when binning using MetaBAT2:

WARNING: bam has improper refpos vs reflen: A00821:285:H3FJHDSXY:4:1362:15049:12399:N:0:GCTGTGAA+GACACTGA#0 pos: 21261 len:14

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[huizhen yan]

Can you help me?

[Rob Egan]

You did not mention how the BAM file was generated. The problem is that whichever tool you used does not do it properly.

If you look at the records in question and work it out by hand, you will find that indeed the record has an incorrect position on the reference (21261), given the reference’s length (14).

This warning it to alert you to the fact that the mapping does not make sense, so you cannot trust the binning that used it.