Open AGI-chandler opened 7 years ago
Addition to the above, only 2 out of 218 LA4Falcon jobs failed with "segmentation fault".
which isn't the full command (missing .las file as last argument)
That's nothing. It's truncated.
/newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/.raw_reads.*
What are the sizes of those files? If not too big, maybe you can get that to me, plus the .las
file. If I can repro, I can fix it.
Otherwise, you need to build a debug version of LA4Falcon and get a stack-trace.
In the meantime, try:
LAshow -a /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/raw_reads.db /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/m_00170/raw_reads.170.las
That might give you a hint. Also try LAdump
. Both should be in your PATH from pitchfork. If that fails, what is the filesize of the .las
file? It might be empty/corrupt.
# du -shc /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/.raw_reads.*
23G /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/.raw_reads.bps
227M /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/.raw_reads.idx
23G total
# du -hsc /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/m_00170/raw_reads.170.las
3.9G /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/m_00170/raw_reads.170.las
3.9G total
#
We could compress it and put it on our FTP if you want.
When I run LAshow and LAdump it spits out a bunch of data... i let it run for a little and it fills up the output file, here is the beginning. Should I let it finish? How could I enable debugging for LA4Falcon?
$ LAshow -a /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/raw_reads.db /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/m_00170/raw_reads.170.las > LAshow.out
^C
$ head LAshow.out
raw_reads.170: 96,777,976 records
4,042,715 87 n [ 18,686.. 20,679] x [ 782.. 2,767] ~ 32.4% ( 644 diffs, 3 trace pts)
18676 ggcgaaccga[atgccaa-cacgaggagcc-tacttcaa-ccatatg-ggactgttgttgagac-cta-caacaa-tc-gtgc-ataa-a--accacaaa
::::::::::[|||||||*||*||||||||*|*||||||*||||||**|||||*||*|||*||**|*|*||||||*||*|*||*|*||*|**||*|||||
772 gaacctgtgg[atgccaagcatgaggagccctgcttcaaaccatataaggact-tt-ttg-gaagcaaacaacaaatctgggcgagaagatgac-acaaa 25.8%
18763 t-cagaggct-g--cacacagttcactgtctcatggtgagagtgccatagaga-t-cattcttcaaa-cagccagt-taatggaaataatgccagt-ctg
$ LAdump /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/raw_reads.db /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/m_00170/raw_reads.170.las > LAdump.out
^C
$ head LAdump.out
+ P 96777976
% P 1756364
+ T -17881080212
% T 130744320
@ T 130744320
P 4042715 87 n .
P 4042715 363 n .
P 4042715 644 n .
P 4042715 936 n .
P 4042715 947 n .
$
Thanks
How could I enable debugging for LA4Falcon?
In DALIGNER
repository directory, rm -f LA4Falcon; CFLAGS=-g make
. I think. You should run something like readlink -f $(which LA4Falcon)
to convince yourself that you are using the rebuild version.
We are experiencing a seg fault with LA4Falcon on our CentOS 6.9 server, using Falcon from pitchfork.
The fault is happening in the
0-rawreads/preads/cns_00170
task:A
core.17702
dump was produced and here is what gdb tells me:I notice the line
Core was generated by 'LA4Falcon -H24386 -fo /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads'.
which isn't the full command (missing.las
file as last argument).The cutoff value produced here is
24386
. So i tried running the command manaully (with more cores so it goes faster, same thing happens with 2,4,8,16 cores...):$ LA4Falcon -H24386 -fo /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/raw_reads.db /newwing/wing2/users/jzhang/work/coarctata/1st/0-rawreads/m_00170/raw_reads.170.las | fc_consensus --output_multi --min_idt 0.70 --min_cov 4 --max_n_read 200 --n_core 40 >| cns_00170.fasta
It runs for a little then crashes again.
LA4Falcon, python2.7, and fc_consensus are all from /opt/pacbio/pitchfork/deployment/bin