[mgblast] FATAL ERROR: CoreLib [001.000] Failed to allocate 67108864 bytes

[QianghuiZhu]

Hi!

While I run Transposome, and I got the following error:

INFO - ======== Transposome version: 0.12.1 (started at: 13-09-2021 09:46:13) ======== INFO - Configuration - Log file for monitoring progress and errors: ERR276219_log.txt INFO - Configuration - Sequence file: ERR276219_interl.fq.gz INFO - Configuration - Sequence format: fastq INFO - Configuration - Sequence number for each BLAST process: 50000 INFO - Configuration - Number of CPUs per thread: 2 INFO - Configuration - Number of threads: 16 INFO - Configuration - Output directory: ERR276219_results_out INFO - Configuration - In-memory analysis: 1 INFO - Configuration - Percent identity for matches: 90 INFO - Configuration - Fraction coverage for pairwise matches: 0.55 INFO - Configuration - Merge threshold for clusters: 0.001 INFO - Configuration - Minimum cluster size for annotation: 100 INFO - Configuration - BLAST e-value threshold for annotation: 10 INFO - Configuration - Repeat database for annotation: /public/home/casdao/kdylvfenghua/kdyzhuqianghui19/data/ARS1/repeat-V2/goats-te-seq.fa INFO - Configuration - Log file for clustering/merging results: ERR276219_cluster_report.txt INFO - Transposome::Run::Blast::run_allvall_blast started at: 13-09-2021 09:46:13. [mgblast] FATAL ERROR: CoreLib [001.000] Failed to allocate 67108864 bytes [mgblast] FATAL ERROR: CoreLib [001.000] Failed to allocate 67108864 bytes [mgblast] FATAL ERROR: CoreLib [001.000] Failed to allocate 67108864 bytes ...

I'm sorry, but is there anything wrong while using mgblast? But it worked well while I run mgblast on command line separately. Is there anything wrong else? Thank you!

[sestaton]

It appears that the program is running out of memory:

 Failed to allocate 67108864 bytes

To confirm, I suggest you downsample the data to a small subset and try again. Typically you only need a small amount of reads (100k - 500k) for accurate predictions.

Please see the examples on the wiki for downsampling sequence files: https://github.com/sestaton/Transposome/wiki/API-Tutorial#seqex3

I am confident that should solve the problem.