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malloc error in first step #12

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NatalieCokel opened this issue Aug 29, 2023 · 0 comments
Open

malloc error in first step #12

NatalieCokel opened this issue Aug 29, 2023 · 0 comments

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@NatalieCokel
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Hello,

I am a master's student working on generating some MAGs for my project, so I'm using metaMIC for assembly quality control before moving onto binning. When running the mapping step, I'm running into the following malloc errors:

bwa(75953,0x700005c90000) malloc: *** error for object 0x60002d897ff0: pointer being freed was not allocated
bwa(75953,0x700005c90000) malloc: *** set a breakpoint in malloc_error_break to debug

Here's the input code that I used:
bwa mem -a -t 8 /Volumes/T7/revisedIC12/assembled/revisedIC12.fasta /Volumes/T7/revisedIC12/trimmomatic/IC12output_1P.fastq /Volumes/T7/revisedIC12/trimmomatic/IC12output_2P.fastq| samtools view -h -q 10 -m 50 -F 4 -b | samtools sort >/Volumes/T7/revisedIC12/sorted/metamicbam.bam

I'm using an iMac macOS Ventura 13.4.1, 64 GB of memory.
I used the conda install and did have some problems downloading the models, so I had to use pip to install job lib, scikit-learn, and requests in order to get the mapping step to run in general.

If there's any advice on how to fix the malloc error, please let me know! I did run first aid in disk utilities prior to trying the mapping step a second time.

Thank you!

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