Segmentation fault (core dumped)

[zhaoxvwahaha]

Hi @rvaser ,

I used racon (v1.4.13) to polish assembly,there are 20+ samples, only 2 of them have the following different problems:
(1)
racon -m 8 -x -6 -g -8 -w 500 -t 8 sample1.porechopQC.filtered_reads.fq.gz sample1.sam sample1.flye.assembly.fasta > sample1.racon.fasta
[racon::Polisher::initialize] loaded target sequences 0.225069 s
[racon::Polisher::initialize] loaded sequences 70.247542 s
[racon::Polisher::initialize] loaded overlaps 18.639637 s
[racon::Polisher::initialize] aligning overlaps [====================] 11.493455 s
Segmentation fault (core dumped)
(2)
racon -m 8 -x -6 -g -8 -w 500 -t 8 sample2.porechopQC.filtered_reads.fq.gz sample2.sam sample2.flye.assembly.fasta > sample2.racon.fasta
[racon::Polisher::initialize] loaded target sequences 0.068931 s
[racon::Polisher::initialize] loaded sequences 64.135422 s
[racon::Polisher::initialize] loaded overlaps 16.719191 s
[racon::Overlap::find_breaking_points] error: overlap is not transmuted!

Could you give some advice, Thanks in advance!
Hailong

[rvaser]

Hi Hailong,
can you paste command which produced sample1.sam and sample2.sam?

Best regards,
Robert

[zhaoxvwahaha]

bwa index 02.flye/Kp819/assembly.fasta
bwa mem 02.flye/Kp819/assembly.fasta 01.porechop_QC/Kp819/Kp819.porechopQC.filtered_reads.fq.gz >03.flye.asmcvg.racon/Kp819/Kp819.sam

[rvaser]

And what is the corresponding racon command? The errors you got indicate that you might misplaced input parameters.

[zhaoxvwahaha]

Hi @rvaser ,the following are racon commands:
(1)
racon -m 8 -x -6 -g -8 -w 500 -t 8 01.porechop_QC/Kp819/Kp819.porechopQC.filtered_reads.fq.gz 03.flye.asmcvg.racon/Kp819/Kp819.sam 02.flye.asmcvg/Kp819/assembly.fasta > 03.flye.asmcvg.racon/Kp819/Kp819.racon.fasta
(2)
racon -m 8 -x -6 -g -8 -w 500 -t 8 01.porechop_QC/Kp95/Kp95.porechopQC.filtered_reads.fq.gz 03.flye.asmcvg.racon/Kp95/Kp95.sam 02.flye.asmcvg/Kp95/assembly.fasta > 03.flye.asmcvg.racon/Kp95/Kp95.racon.fasta

[rvaser]

The commands look fine, if the 03.flye.asmcvg.racon/Kp95/Kp95.sam file was generated with 02.flye.asmcvg/Kp95/assembly.fasta and 01.porechop_QC/Kp95/Kp95.porechopQC.filtered_reads.fq.gz. Is it possible for you to share those two assemblies and corresponding reads, so I can see what is happening?

[zhaoxvwahaha]

@rvaser
yes, but how could I share the data to you, the data size is big (~2.5G)

[rvaser]

Dropbox? Google drive? Not sure :/