Starting with cortex_var

[covux]

hey,

I am kinda of new to bioinformatics and for a project i need to use some variant callers and compare them.

Now i have came across cortex_var and wanted to give it a try.

but i am encountering the following problem:

Error: Dear user - you have not allocated enough memory to contain your sequence data. Either allocate more memory (have you done your calculations right? have you allowed for sequencing errors?), or threshold more harshly on quality score, and try again. Aborting mission.

i am trying to make the following command line work:

cortex_var_31_c1 --pe_list E_coli_PE_list_1,E_coli_PE_list_2 --kmer_size 31 -- quality_score_threshold 15 --remove_low_coverage_supernodes 10 --max_read_len 10000 --mem_height = 25 - -mem_width=100 --output_bubbles1 bubbles_called_from_genome


i am working with an E.coli from NCBI ( SRR1770413).

i have changed the numbers for the quaility score, mem height, mem width and use remove_low_coverage_supernodes but i keep getting the same message.

if there something i am overlooking?


Regards,
covux

[Zamin Iqbal]

Hi Covux

 

Error: Dear user - you have not allocated enough memory to contain your sequence data. Either allocate more memory (have you done your calculations right? have you allowed for sequencing errors?), or threshold more harshly on quality score, and try again. Aborting mission.

i am trying to make the following command line work:

cortex_var_31_c1 --pe_list E_coli_PE_list_1,E_coli_PE_list_2 --kmer_size 31 -- quality_score_threshold 15 --remove_low_coverage_supernodes 10 --max_read_len 10000 --mem_height = 25 - -mem_width=100 --output_bubbles1 bubbles_called_from_genome

So, for mem_height and mem_width alone, you have equals signs

ie you have

 --mem_height = 25

not 

 --mem_height 25

For all the othr arguments you have it right.

 

i am working with an E.coli from NCBI ( SRR1770413).

For E coli, you don't need much memory at all. mem height/width of 25 and 100 is masses of memory - enough for  a human genome.

I would expect

--mem_height 18 --mem_width 100 

would be plenty

 

regards

Zam 

[covux]

Zam,

you are right.
the day after i send you a message i toke another look and saw the flaws in my command line.


how ever if i use the next command line:

cortex_var_31_c1 --pe_list E_coli_PE_list_1,E_coli_PE_list_2 --kmer_size 31 -- quality_score_threshold 15 --remove_low_coverage_supernodes 10 --max_read_len 10000 --mem_height 18 --mem_width 100 --output_bubbles1 bubbles_called_from_genome


i still get this error message.

Mon May 15 16:52:38 2017

Error: Dear user - you have not allocated enough memory to contain your sequence data. Either allocate more memory (have you done your calculations right? have you allowed for sequencing errors?), or threshold more harshly on quality score, and try again. Aborting mission.

When i look into NCBI SRA i see this

Run

	# of Spots	# of Bases	Size	Published
SRR1770413	643,253	387.2M	189.9Mb	2015-01-24