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This is not a problem, merely a warning |
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Hello everyone,
I am using SPADes to create assemblies from Illumina reads of mammalian DNA (with no reference, as by now it is currently unavailable for the species).
System information:
SPAdes version: 3.15.5
Python version: 3.10.4
Initially I didn`t encounter any problem, outside few warnings that were however caused by the quality of the used data. Using the same script, since I know it works just fine, I started working on sequences from the same species obtained from a different illumina sequencing batch, and for every try I have done so far I have always encountered the same issue with the "PairInfoImprover" step.
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INFO PairInfoImprover (pair_info_improver.hpp : 104) Paired info stats: missing = 176986572; contradictional = 213580
mimalloc: warning: unable to allocate from region: size 4194304
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This issue was encountered using as a input material both untrimmed and trimmed R1 and R2 (through Trimmomatic).
From what I have understood, the problem could be either with the quality of the reads themselves or with not enough memory being available for the task. In the log file, however, the log file reports no failure for the script run and no additional warnings, and all requested outputs file are being produced.
Regarding possible memory issues, I tried with the following:
cpus-per-task=16
mem-per-cpu: 25, or 40, or 60, or 80 G
-m 400
but I always obtained the same exact issue. I wanted to ask if there is actually anything I could do to resolve this?
Many thanks.
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