Pointer Error running MetaBAT 2 (v2.13 (Bioconda))

[Nick Waters]

Hello,

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I am getting the following error after assembling with megahit, mapping with bwa mem, and using samtools to sort and index the BAM file:

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 $ jgi_summarize_bam_contig_depths --outputDepth tmp/mapping_depth.txt tmp/mapping_sorted.bam
 $ metabat2  --inFile ./tmp/megahit/final.contigs.fa --outFile tmp/metabat/ --abdFile tmp/mapping_depth.txt -v
MetaBAT 2 (v2.13 (Bioconda)) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, and maxEdges 200.
[00:00:00] Finished reading 16 contigs and 1 coverages from tmp/mapping_depth.txt
[00:00:00] Number of target contigs: 11 of large (>= 2500) and 1 of small ones (>=1000 & <2500).
[00:00:00] Finished TNF calculation.
[00:00:00] Finished Preparing TNF Graph Building [pTNF = 95.60]
metabat2(41636,0x700000d0a000) malloc: *** error for object 0x407688abceec3535: pointer being freed was not allocated
metabat2(41636,0x700001d16000) malloc: *** error for object 0xa: pointer being freed was not allocated
metabat2(41636,0x700000d0a000) malloc: *** set a breakpoint in malloc_error_break to debug
metabat2(41636,0x700000907000) malloc: *** error for object 0xa: pointer being freed was not allocated
metabat2(41636,0x70000110d000) malloc: *** error for object 0xa: pointer being freed was not allocated
metabat2(41636,0x700001913000) malloc: *** error for object 0x407688abceec3535: pointer being freed was not allocated
metabat2(41636,0x700001d16000) malloc: *** set a breakpoint in malloc_error_break to debug
metabat2(41636,0x70000110d000) malloc: *** set a breakpoint in malloc_error_break to debug
metabat2(41636,0x700001913000) malloc: *** set a breakpoint in malloc_error_break to debug
metabat2(41636,0x700000907000) malloc: *** set a breakpoint in malloc_error_break to debug

I have attached the relevant files. I get tthe same error running metabat2 or runMetaBat2.sh. This is my first time trying metabat; is there something wrong with my input files?

[Nick Waters]

Contigs

[Nick Waters]

Depths file

[Rob Egan]

Hi,

I am unable to replicate your problem on my machine using the latest versionv2.13-29-g2e72973

The bioconda build is not maintained by our group, so please use the latest version from docker or build it with cmake & boost dependencies.

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./metabat2 --inFile final.contigs.fa --outFile test22 --abdFile mapping_depth.txt -v --seed 0
MetaBAT 2 (v2.13-29-g2e72973) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, and maxEdges 200. 
[00:00:00] Executing with 40 threads
[00:00:00] Parsing abundance file
[00:00:00] Parsing assembly file
[00:00:00] Number of large contigs >= 2500 are 11. 
[00:00:00] Reading abundance file
[00:00:00] Finished reading 16 contigs and 1 coverages from ../mapping_depth.txt
[00:00:00] Number of target contigs: 11 of large (>= 2500) and 1 of small ones (>=1000 & <2500). 
[00:00:00] Start TNF calculation. nobs = 11
[00:00:00] Finished TNF calculation.                                  
[00:00:00] Finished Preparing TNF Graph Building [pTNF = 95.40]                                             
[00:00:00] Finished Building TNF Graph (21 edges) [6.9Gb / 251.8Gb]                                          
[00:00:00] Building SCR Graph and Binning (11 vertices and 11 edges) [P = 95.00%; 6.9Gb / 251.8Gb]                           
[00:00:00] Outputting bins
[00:00:00] 100.00% (228245 bases) of large (>=2500) and 0.00% (0 bases) of small (<2500) contigs were binned.
1 bins (228245 bases in total) formed.
[00:00:00] Finished

[Rob Egan]

Please resubmit if the latest version does not solve the problem.

[Nick Waters]

Hi Rob, I’m so sorry, I missed the ping there in July; thanks for looking into to!