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Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Hello,
I can't compile SOAP
g++: warning: ‘-mcpu=’ is deprecated; use ‘-mtune=’ or ‘-march=’ instead
g++: error: unrecognized command line option ‘-maltivec’; did you mean ‘-mglibc’?
make: *** [<builtin>: 2bwt-lib/BWTConstruct.o] Error 1
neither BGS
g++ -O3 -funroll-loops -w -fopenmp -D__STDC_LIMIT_MACROS -mcpu=power8 -mtune=power8 -maltivec -fsigned-char -c -o 2bwt-lib/BWT.o 2bwt-lib/BWT.c
g++: warning: ‘-mcpu=’ is deprecated; use ‘-mtune=’ or ‘-march=’ instead
g++: error: unrecognized command line option ‘-maltivec’; did you mean ‘-mglibc’?
With gcc 6.3.1
~/src_naibin/16GT$ make
g++ -O3 -funroll-loops -fomit-frame-pointer -maccumulate-outgoing-args -funroll-loops -static-libgcc -mpopcnt -fopenmp -fpermissive -w snapshotSnpcaller.o SNP.o SAMhandler.o FisherExactTest.o VariantCaller.o SnapshotHandler.o fisher.o likelihood_cache.o ycsq.o SNP_Caller.o SNPFunctions.o interpreter.o lib/lib.a -lpthread -lm -lz -o snapshotSnpcaller
/usr/bin/ld: lib/lib.a(BWT.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(CPUfunctions.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(DNACount.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(HSP.o): relocation R_X86_64_32S against
.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(HSPstatistic.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(MemManager.o): relocation R_X86_64_32 against
.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(MemoryCounter.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(MiscUtilities.o): relocation R_X86_64_32S against
.bss' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(PEAlgnmt.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(PE.o): relocation R_X86_64_32S against
.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(r250.o): relocation R_X86_64_32 against .bss' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(TextConverter.o): relocation R_X86_64_32S against
.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(Timing.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(SimpleMemoryPool.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(IniParam.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(iniparser.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(inistrlib.o): relocation R_X86_64_32 against .bss' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(bam.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(bam_import.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(sam_header.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(AlgnResult.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(BGS-HostAlgnmtAlgo.o): relocation R_X86_64_32 against
.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(BGS-HostAlgnmtAlgo2.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(BGS-HostAlgnmtAlgoSingle.o): relocation R_X86_64_32 against
.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(BGS-HostAlgnmtOps.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(BGS-IO.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(Indel_RA.o): relocation R_X86_64_32 against symbol _Z23identifyRAWindowWrapperPv' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(ScoreRecalibration.o): relocation R_X86_64_32S against
.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(SNPDuplicateRemoval.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(dictionary.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(PrimerHashAPI.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(bgzf.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(bam_aux.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(sam.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(bam_pileup.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(faidx.o): relocation R_X86_64_32 against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: lib/lib.a(knetfile.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /usr/bin/ld: lib/lib.a(razf.o): relocation R_X86_64_32S against
.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:11: recipe for target 'snapshotSnpcaller' failed
make: *** [snapshotSnpcaller] Error 1
Thanks for your kind help to diagnose the error shown here.
Hello,
I've got a problem using the snapshotSnpcaller:
Loading reference index...
Done in 6.3894 seconds
Reference sequence length: 1255676862Reading snapshot...
Read snapshot in 10.8167 secondsHandling SNP Counter Result
MMUnitAllocate() : cannot allocate memory!
It can't allocate memory but I'm not sure why.
Thank you for your help,
David
Hello,
I'm on mac os 10.15.4 (Catalina) trying to install 16GT.
My clang version: Apple clang version 11.0.3 (clang-1103.0.32.59)
I have latest gcc (g++-9)
My try:
$ git clone https://github.com/aquaskyline/16GT
$ cd 16GT
$ make
g++ -O3 -funroll-loops -fomit-frame-pointer -maccumulate-outgoing-args -funroll-loops -static-libgcc -mpopcnt -fopenmp -fpermissive -w -c snapshotSnpcaller.cpp -o snapshotSnpcaller.o
clang: error: unknown argument: '-maccumulate-outgoing-args'
clang: error: unsupported option '-fopenmp'
make: *** [snapshotSnpcaller.o] Error 1
Thank you in advance :-)
Could you explain better the steps? I find information missing,
-what type of bam does it need to work, sorted, mark duplicates, BQSR?
-can the bam file be produced with any mapper or only SOAP3-dp?
-what is the.bin file?
-what does each step do?
-If I have a bam file and the reference.fasta indexed where should I start?
Thank you very much
~/16GT> /home/tao/16GT/bam2snapshot -i /home/tao/seq/jelly_out_chr_pilon.fasta.rename.fa.index -b /home/newdisk/tao/z_final_new/432.sort.bam -b /home/newdisk/tao/z_final_new/ZGWS.sort.bam -b /home/newdisk/tao/z_final_new/543.sort.bam -b /home/newdisk/tao/z_final_new/ZO1.sort.bam -b /home/newdisk/tao/z_final_new/AL1.sort.bam -b /home/newdisk/tao/z_final_new/PZ.sort.bam -b /home/newdisk/tao/z_final_new/BG.sort.bam -b /home/newdisk/tao/z_final_new/PZHBL.sort.bam -b /home/newdisk/tao/z_final_new/BYDHL.sort.bam -b /home/newdisk/tao/z_final_new/QBL.sort.bam -b /home/newdisk/tao/z_final_new/DH2.sort.bam -b /home/newdisk/tao/z_final_new/SRR2131192.sort.bam -b /home/newdisk/tao/z_final_new/FH.sort.bam -b /home/newdisk/tao/z_final_new/T1-6.sort.bam -b /home/newdisk/tao/z_final_new/HLJHL.sort.bam -b /home/newdisk/tao/z_final_new/WSHL.sort.bam -b /home/newdisk/tao/z_final_new/JX.sort.bam -b /home/newdisk/tao/z_final_new/XHHL.sort.bam -b /home/newdisk/tao/z_final_new/XL.sort.bam -o /home/newdisk/tao/z_final_new/16GTotherlotus
Loading reference...
Done.
464 chromosomes, 821160161bp in length.
Parameters:
#CPUThreads=16
TrimSize=5
SoftClipThreshold=5
MQThreshold=0
indelWeightThreshold=1
Allocating memory...
Done.
Time elapsed by now is 0 seconds.
Updating snapshot...
Processing /home/newdisk/tao/z_final_new/432.sort.bam...
Segmentation fault (core dumped)
Dear friend, you tool does not have any parameters for changing the number of threads.
Please let us know how to set it!
Hi @aquaskyline
I have two questions about 16GT. First, does it support trio joint calling? Can I use all the samples as the input of bam2snapshot? Second, is it compatible with the hs38dh reference genome? Is there something like the BadMateFilter in GATK that will cause problems when calling variants on the ALT contigs?
Thanks
Hello, I have tried to follow the tutorial in the README file, but program bam2snapshot
have dropped a a Segmentation fault. Here is gdb
output :
...
Processing ref_is350_to_b3v06_masked_div30.bam...
Program received signal SIGSEGV, Segmentation fault.
0x0000000000418670 in getAmbPos (chr_id=0, offset=1, ambiguityMap=ambiguityMap@entry=0x6582c0,
translate=translate@entry=0x7ffff7f4c010, dnaLength=982460096) at indexFunction.cpp:22
22 while (translate[approxValue].startPos > ambPos) {
The bam file is rather big, but privately I can share it if needed.
--- edit ---
Some technical details. It's a sorted bamfile, reads were mapped using bwa-mem
and PCR duplicates were marked using samblaster
. I am running it on CentOS 7
, compiled using gcc version 6.1.1
.
Hi. I've downloaded and installed 16GT and plan to call somatic mutations. However, I can not find the proper command to call. Would somebody could tell me about that? Thank you.
Hi, Is variant calling on RNA supported?
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