Question: Oases pipeline fails on second kmer
0
gravatar for katie.duryea
3.2 years ago by
katie.duryea30
katie.duryea30 wrote:

Hello all,

I am hoping for help running the oases_pipeline.py. I am able to run the pipeline for a subset of my data and for 4 Kmer values using the following code:

python oases_pipeline.py -m 21 -M 27 -s 2 -o oases_test -d '-fastq -shortPaired -separate trimm_15_F_paired.fq trimm_15_R_paired.fq' -p '-ins_length 160'

This runs successfully and produces output for K 21 through 27. However, when I try to run the following code on my full dataset (538769828 sequences) and for a larger range of K, it fails. This is my input code:

python oases_pipeline.py -m 21 -M 51 -s 2 -o oases_ALL -d '-fastq -shortPaired -separate ALL_F_paired.fq ALL_R_paired.fq' -p '-ins_length 160' 

This command runs successfully for K=21, but then crashes on K=23 with this output:

[5141.379366] Inputting sequence 66000000 / 538769828

[5163.243577] Inputting sequence 67000000 / 538769828

[5170.824776]  === Sequences loaded in 997.337692 s

[5171.829179] Done inputting sequences

[5171.829187] Destroying splay table

[5173.870477] Splay table destroyed

[5175.177294] Command failed!

[5175.177304] rm -f oases_ALL_23/Sequences

Hash failed

I am at a loss for why it will run for a subset of data and for the first K, but crash on the second. 

Many thanks in advance for any input!

rna-seq forum • 707 views
ADD COMMENTlink modified 3.2 years ago by ayushiyakshi0 • written 3.2 years ago by katie.duryea30
0
gravatar for katie.duryea
3.2 years ago by
katie.duryea30
katie.duryea30 wrote:

UPDATE: I got this run by changing the step size (s) to 4. I'm not sure why that worked, so I will leave this up here in case someone else encounters this problem or has input on what is happening.

ADD COMMENTlink written 3.2 years ago by katie.duryea30
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