Memory issue causes R aborting

[lam-c]

Hi, developer,

Thank you for bring us this great tool. I tried das tool 1.1.7 within a singularity image and encountered a segfault error. I'm sorry that I can't pinpoint what is going wrong. And look forward for your advice to help me solve this problem.

Best regards,

These information might help with troubleshooting:

System: Red Hat 8.5.0-10
singularity-ce version 3.10.2-1.el8
singularity image: quay.io-biocontainers-das_tool-1.1.7--r43hdfd78af_0.img

$ DAS_Tool \
    --write_bins --write_unbinned --write_bin_evals --score_threshold 0.5 \
    -t 20 \
    -i SPAdes-MetaBAT2-S21.tsv,SPAdes-MaxBin2-S21.tsv,SPAdes-CONCOCT-S21.tsv \
    -c SPAdes-S21_scaffolds.fasta \
    -o SPAdes-DASTool-S21

# stderr (full stdout and stderr could be found in attachments)
 *** caught segfault ***
address 0x7f8035300298, cause 'invalid permissions'
address 0x7f8034effdb0, cause 'invalid permissions'
Error in forderv(x, cols, sort = TRUE, retGrp = FALSE) : bad value
Calls: [ ... [.data.table -> .prepareFastSubset -> setkeyv -> forderv
Execution halted
Error: bad value

Traceback:
 1: forderv(x, cols, sort = TRUE, retGrp = FALSE)
 2: setkeyv(i, idxCols)
 3: Fatal error: error during cleanup

.prepareFastSubset(isub = isub, x = x, enclos = parent.frame(),     notjoin = notjoin, verbose = verbose)
 4: `[.data.table`(binTab, !contig_id %in% contigTab[, contig_id])
 5: binTab[!contig_id %in% contigTab[, contig_id]]
An irrecoverable exception occurred. R is aborting now ...
rm: can't remove '/tmp/RtmpO0pmqG': No such file or directory
rm: can't remove '/tmp/RtmpO0pmqG': No such file or directory
rm: can't remove '/tmp/RtmpO0pmqG': No such file or directory
rm: can't remove '/tmp/RtmpO0pmqG': No such file or directory
/usr/local/bin/DAS_Tool: line 34:    52 Segmentation fault      (core dumped) Rscript --vanilla ${DIR}/src/DAS_Tool.R

stdout.txt stderr.txt

[mengyuan09876]

Hi, I have the same error as yours. Did you finally solved it？

[abdo3a]

Hello @lam-c @mengyuan09876 Did you solve this issue, I'm have the same one.