[M::mem_pestat] mean and std.dev: (272.64, 66.53)
[M::mem_pestat] low and high boundaries for proper pairs: (7, 539)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 28 reads in 0.045 CPU sec, 0.018 real sec
[main] Version: 0.7.17-r1198-dirty
[main] CMD: /mypath/Scaff10X/src/scaff-bin/bwa mem -p -t 30 tarseq.fastq -
[main] Real time: 2.431 sec; CPU: 2.265 sec
sh : ligne 1 : 11840 segmentation fault /mypath/Scaff10X/src/scaff-bin/scaff_bwa -edge 50000 tarseq.tag align.dat align2.dat > try.out
Error running command: /mypath/scaff_bwa -edge 50000 tarseq.tag align.dat align2.dat > try.out
Input target assembly file2: /mypath/contigs-break.fasta
www: /mypath/input.dat input.dat
Input data file: /mypath/input.dat
/mypath/Scaff10X/src/scaff-bin/scaff_FilePreProcess -t 2 -n 1 /mypath/input.dat - |/mypath/Scaff10X/src/scaff-bin/bwa mem -p -t 30 tarseq.fastq - | egrep tarseq_ | awk '($2<100)&&($5>=0){print $1,$2,$3,$4,$5}' | egrep -v '^@' > align.dat
/mypath/scaff10x/Scaff10X/src/scaff-bin/scaff_bwa -edge 50000 tarseq.tag align.dat align2.dat > try.out
I tried to launch it several times.
We did not get any out of memory error.
Instead of input.dat I tried to put directly the fastq. Here, I run it on the result of break10x but I also tried on another assembly.
So we tried to find where the error is by modifying the src/makefile by adding the following flag :
AddressSanitizer:DEADLYSIGNAL
=41390==ERROR: AddressSanitizer: SEGV on unknown address 0x000000000001 (pc 0x7f8c98704721 bp 0x7ffd69f98740 sp 0x7ffd69f97ed8 T0)
==41390==The signal is caused by a READ memory access.
==41390==Hint: address points to the zero page.
#0 0x7f8c98704721 in __strlen_sse2_pminub (/lib64/libc.so.6+0x16f721)
#1 0x433f33 in __interceptor_strcpy ../../.././libsanitizer/asan/asan_interceptors.cpp:437
#2 0x406e52 in main /mypath/src/scaff_bwa.c:220
#3 0x7f8c985b7554 in __libc_start_main (/lib64/libc.so.6+0x22554)
#4 0x407006 (/mypath/Scaff10X/src/scaff-bin/scaff_bwa+0x407006)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV (/lib64/libc.so.6+0x16f721) in __strlen_sse2_pminub
Do you have an idea for the resolution of this problem?
It seems that your code (scaff_bwa.c, line 220) is expecting a _ in align.dat, but there is none.
Dear developers,
we are running
Scaff10x V.5
with the following command:My
input.dat
is:and we obtain the following error message:
I tried to launch it several times. We did not get any out of memory error. Instead of
input.dat
I tried to put directly the fastq. Here, I run it on the result of break10x but I also tried on another assembly.So we tried to find where the error is by modifying the
src/makefile
by adding the following flag :like this:
we run the command that causes the problem in
tmp_rununik
repertory :and we obtain:
Do you have an idea for the resolution of this problem? It seems that your code (
scaff_bwa.c
, line 220) is expecting a_
inalign.dat
, but there is none.Thank you!