- Windows 10
- Running in Terminal
I'm working on a non-model organism. I concatenated two samples raw reads (larval and adult), and used Galaxy Trinity to assemble the concatenated forward and reverse strands.
I then ran kallisto index on the fasta file (~107,500 KB)
kallisto index -i I.f_concat_Trinity_assembled.index I.f_concat_Trinity_assembled.fasta
This generates a file (size 1,186,659 KB) with the following log
[build] loading fasta file I.fasciola_109A1_67B8_concat_Trinity_assembled.fasta [build] k-mer length: 31 [build] warning: clipped off poly-A tail (longer than 10) from 78 target sequences [build] counting k-mers ... done. [build] building target de Bruijn graph ... done [build] creating equivalence classes ... done [build] target de Bruijn graph has 512211 contigs and contains 54818622 k-mers
When I run kallisto quant using the index file
kallisto quant \ -i I.f_concat_Trinity_assembled.index \ -o 67B6 \ -t 4 \ 67B6_1.fq.gz \ 67B6_2.fq.gz \ &> 67B6.log
I get the following log and error message
[quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 175,677 [index] number of k-mers: 54,818,622 [index] number of equivalence classes: 65,536 terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc
I have no idea how to fix this problem. I have run kallisto using practise human files and it worked so I can't quite work out what's going wrong. Googling tells me I may not have enough memory, but I have over 100 GB storage free, and 16 GB RAM. The human index I generated and aligned to was 2,445,321 KB (over twice the size), so really size shouldn't be a problem.
What is std::bad_alloc? How do I fix it?