mapping with bfast killed when created index
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Entering edit mode
6 weeks ago
Lila M ★ 1.1k

Hi there, I'm doing some alignments using colour space files (downloaded from sra) But I'm stuck because the process is kill and I do not have experience in colourspace files. What I've done so far is

Convert the reference (color space):

$bfast fasta2brg -f hg38.fa -A 1 

Create the indexes:

$bfast index -f hg18.fa -m 1111111111111111111111 -w 14 -i 1 -A 1

(I'm using the mask suggested in the manual)

But after a while, I got this log:

Checking input parameters supplied by the user ...
Validating fastaFileName GRCh38.p10.genome.fa. 
Validating tmpDir path ./. 
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode:                [ExecuteProgram]
fastaFileName:              GRCh38.p10.genome.fa
space:                  [Color Space]
mask:                   111111110001111110011111111
depth:                  0
hashWidth:              14
indexNumber:                5
repeatMasker:               [Not Using]
startContig:                0
startPos:               0
endContig:              2147483647
endPos:                 2147483647
exonsFileName:              [Not Using]
numThreads:             1
tmpDir:                 ./
timing:                 [Not Using]
************************************************************
************************************************************
Reading in reference genome from GRCh38.p10.genome.fa.cs.brg.
In total read 555 contigs for a total of 3236815040 bases
************************************************************
Creating the index...
************************************************************
Warning: startContig was less than zero.
Defaulting to contig=1 and position=1.
************************************************************
************************************************************
Warning: endContig was greater than the number of contigs in the reference genome.
Defaulting to reference genome's end contig=555 and position=71251.
************************************************************
Currently on [contig,pos]:
[-----555,------71251]
Sorting...
50.000 percent complete
Killed

Any help would be great! Thanks!

bfast mapping index • 135 views
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The Killed signal could be because you reached maximal memory allowed, or CPU or disk space, are you running this on a cluster?

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thank you for the tip. Not, I'm running it locally, but I've never had this kind of problems before with human genome

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even on local run, check if there are limits to memory or cpu usage

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