Comments (15)
kingralph80
commented on May 24, 2024
Hi, I cloned the latest src from github and compile it and tried it. I runs further but now I get:
Binary seq file = /netscratch/dep_psl/grp_frommer/Michael_Thomas/Genomes/Zea_mays/custom/AGPvZm00001d032854/Zm00001d032854.Oh43.fa.0123
Reference genome size: 526 bp
Done readng reference genome !!
[0000] 1: Calling process()
Threads used (compute): 60
Info: projected #read in a task: 3973519
Memory pre-allocation for chaining: 8360.2840 MB
Memory pre-allocation for BSW: 14377.0214 MB
Memory pre-allocation for BWT: 4638.8506 MB
No. of pipeline threads: 2
[0000] read_chunk: 600000000, work_chunk_size: 600000012, nseq: 8042716
[0000][ M::kt_pipeline] read 8042716 sequences (600000012 bp)...
Reallocating initial memory allocations!!
[0000] 2. Calling mem_process_seqs.., task: 0
[0000] 3. Calling kt_for - worker_bwt
[0000] 3. Calling kt_for - worker_aln
Error: This should not have happened!!!
Error: assert failed for seqPair size, numPairsLeft: 0, numPairsRight 0
Exiting.
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kingralph80
commented on May 24, 2024
Also: Thread model: posix
gcc version 6.3.0 20170516 (Debian 6.3.0-18+deb9u1)
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yuk12
commented on May 24, 2024
It says, "Reference genome size: 526 bp" -- is that correct?
if yes, can you share the reads and reference genome? we will look into this.
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kingralph80
commented on May 24, 2024
It's actually 2x the size. Its something I did notice also when I use the full length genome. The size I get when I run bwa-mem2 index is always 2x the expected size. I can upload the genome and a subset of the fastq to google drive. How to share?
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yuk12
commented on May 24, 2024
You can share the link here. Thanks
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ybx-818
commented on May 24, 2024
Hi,do you have solved this problem ? I also get into this trouble.when i use bwa-men2 to align reference genome and illumina raw data ,it's ok .but when i first filter the raw data by Fastp, it's error.I don't find the reason cased this trouble ,can you help me ? Thanks for you !
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yuk12
commented on May 24, 2024
Can you share a small sample of the data causing this problem?
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ybx-818
commented on May 24, 2024
sorry ,the data I use to analyze is 1.5GB, it's too large. I don't know how to split a small sample .Thanks.
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yuk12
commented on May 24, 2024
Are you using the same genome of size: 526 bp?
About reads data. Can you share the first 10 million sequences? In fastq files each sequence occupies 4 lines so you get first 10 million seqs as: head -n 4000000 <in.fastq> > <out.fastq>
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ybx-818
commented on May 24, 2024
No, the size of genome I used to analyze is 42M, and I get first 10 million seqs ,the size of it is 350M. it's too large for share .I thought the error is caused by the change of filtering with Fastp. Thanks.
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ybx-818
commented on May 24, 2024
I get the same error at #1 , and they have solved this problem. But I can't understand how to do.
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sanchit-misra
commented on May 24, 2024
#1 has got resolved. Could you please try the latest commit?
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ybx-818
commented on May 24, 2024
I used the precompiled binaries at first. (My system is ubuntu 18.04 LTS) In order to solve the trouble, I dowmload the bwa-mem2 and encounter the error when runing "make" command.
if (isAwesome){
return true
}
:~/software/bwa-mem2# make
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIpp -o src/fastmap.o
src/fastmap.cpp: In function ‘int64_t get_limit_fsize(FILE*, int64_t, char*
src/fastmap.cpp:120:10: warning: ignoring return value of ‘char* fgets(char
fgets((char*) buf1, len, fpp);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
src/fastmap.cpp:121:10: warning: ignoring return value of ‘char* fgets(char
fgets((char*) buf1, len, fpp);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
src/fastmap.cpp: In function ‘int main_mem(int, char**)’:
src/fastmap.cpp:921:8: warning: ignoring return value of ‘size_t fread(voidsed-result]
fread(ref_string, 1, rlen, fr);
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIcpp -o src/bwtindex.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAI -o src/utils.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIpp -o src/kthread.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIpp -o src/kstring.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIo src/ksw.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIp -o src/bntseq.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIp -o src/bwamem.o
src/bwamem.cpp: In function ‘void mem_process_seqs(mem_opt_t*, const bntseq:
src/bwamem.cpp:1278:68: warning: '0' flag ignored with precision and ‘%d’ g
fprintf(stderr, "[%0.4d] 3. Calling kt_for - worker_bwt\n", myrank);
^
src/bwamem.cpp:1282:68: warning: '0' flag ignored with precision and ‘%d’ g
fprintf(stderr, "[%0.4d] 3. Calling kt_for - worker_aln\n", myrank);
^
src/bwamem.cpp:1302:69: warning: '0' flag ignored with precision and ‘%d’ g
fprintf(stderr, "[%0.4d] 10. Calling kt_for - worker_sam\n", myrank);
^
src/bwamem.cpp:1309:54: warning: '0' flag ignored with precision and ‘%d’ g
__func__, n, cputime() - ctime, realtime() - rtime);
^
src/bwamem.cpp: In function ‘void mem_chain2aln_across_reads_V2(const mem_oeg_v*, mem_cache*, int64_t, int64_t, int64_t, int)’:
src/bwamem.cpp:2013:38: warning: invalid conversion from ‘int’ to ‘_mm_hint
_mm_prefetch((const char*) query, 0);
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:3
from src/bandedSWA.h:42,
from src/bwamem.h:39,
from src/bwamem.cpp:31:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:52:1: note: initializ
_mm_prefetch (const void *__P, enum _mm_hint __I)
^~~~~~~~~~~~
src/bwamem.cpp:2031:52: warning: invalid conversion from ‘int’ to ‘_mm_hint
_mm_prefetch((const char*) (srtg + spos + 64), 0);
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:3
from src/bandedSWA.h:42,
from src/bwamem.h:39,
from src/bwamem.cpp:31:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:52:1: note: initializ
_mm_prefetch (const void *__P, enum _mm_hint __I)
^~~~~~~~~~~~
src/bwamem.cpp:2032:41: warning: invalid conversion from ‘int’ to ‘_mm_hint
_mm_prefetch((const char*) (lim_g), 0);
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:3
from src/bandedSWA.h:42,
from src/bwamem.h:39,
from src/bwamem.cpp:31:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:52:1: note: initializ
_mm_prefetch (const void *__P, enum _mm_hint __I)
^~~~~~~~~~~~
src/bwamem.cpp:2069:38: warning: invalid conversion from ‘int’ to ‘_mm_hint
_mm_prefetch((const char*) rseq, 0);
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:3
from src/bandedSWA.h:42,
from src/bwamem.h:39,
from src/bwamem.cpp:31:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:52:1: note: initializ
_mm_prefetch (const void *__P, enum _mm_hint __I)
^~~~~~~~~~~~
src/bwamem.cpp:2129:77: warning: '0' flag ignored with precision and ‘%d’ g
fprintf(stderr, "[LOG][%0.4d] Re-allocating seqPairArrays Left\n", t
src/bwamem.cpp:2204:79: warning: '0' flag ignored with precision and ‘%d’ g
fprintf(stderr, "[LOG] [%0.4d] Re-allocating seqPairArrays Right\n",
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAI.cpp -o src/profiling.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAI.cpp -o src/bandedSWA.o
src/bandedSWA.cpp: In member function ‘void BandedPairWiseSW::smithWaterman
src/bandedSWA.cpp:3755:64: warning: invalid conversion from ‘int’ to ‘_mm_h
_mm_prefetch((const char*) seqBufRef + (int64_t)spf.idr, 0);
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:3
from src/bandedSWA.h:42,
from src/bandedSWA.cpp:30:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:52:1: note: initializ
_mm_prefetch (const void *__P, enum _mm_hint __I)
^~~~~~~~~~~~
src/bandedSWA.cpp:3756:69: warning: invalid conversion from ‘int’ to ‘_mm_h
_mm_prefetch((const char*) seqBufRef + (int64_t)spf.idr + 64, 0);
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:3
from src/bandedSWA.h:42,
from src/bandedSWA.cpp:30:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:52:1: note: initializ
_mm_prefetch (const void *__P, enum _mm_hint __I)
^~~~~~~~~~~~
src/bandedSWA.cpp:3799:64: warning: invalid conversion from ‘int’ to ‘_mm_h
_mm_prefetch((const char*) seqBufQer + (int64_t)spf.idq, 0);
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:3
from src/bandedSWA.h:42,
from src/bandedSWA.cpp:30:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:52:1: note: initializ
_mm_prefetch (const void *__P, enum _mm_hint __I)
^~~~~~~~~~~~
src/bandedSWA.cpp:3800:69: warning: invalid conversion from ‘int’ to ‘_mm_h
_mm_prefetch((const char*) seqBufQer + (int64_t)spf.idq + 64, 0);
^
In file included from /usr/lib/gcc/x86_64-linux-gnu/7/include/emmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/pmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/tmmintrin.h:3
from /usr/lib/gcc/x86_64-linux-gnu/7/include/smmintrin.h:3
from src/bandedSWA.h:42,
from src/bandedSWA.cpp:30:
/usr/lib/gcc/x86_64-linux-gnu/7/include/xmmintrin.h:52:1: note: initializ
_mm_prefetch (const void *__P, enum _mm_hint __I)
^~~~~~~~~~~~
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIh.cpp -o src/FMI_search.o
src/FMI_search.cpp: In constructor ‘FMI_search::FMI_search(char*)’:
src/FMI_search.cpp:55:10: warning: ignoring return value of ‘size_t fread(vunused-result]
fread(&reference_seq_len, sizeof(int64_t), 1, cpstream);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/FMI_search.cpp:65:10: warning: ignoring return value of ‘size_t fread(vunused-result]
fread(&count[0], sizeof(int64_t), 5, cpstream);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/FMI_search.cpp:68:10: warning: ignoring return value of ‘size_t fread(vunused-result]
fread(cp_occ, sizeof(CP_OCC), cp_occ_size, cpstream);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/FMI_search.cpp:76:10: warning: ignoring return value of ‘size_t fread(vunused-result]
fread(sa_ms_byte, sizeof(int8_t), reference_seq_len, cpstream);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/FMI_search.cpp:77:10: warning: ignoring return value of ‘size_t fread(vunused-result]
fread(sa_ls_word, sizeof(uint32_t), reference_seq_len, cpstream);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIx_ele.cpp -o src/read_index_ele.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIir.cpp -o src/bwamem_pair.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAI-o src/kswv.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIo src/bwa.o
src/bwa.cpp: In function ‘bseq1_t* bseq_read(int64_t, int*, void*, void*, F
src/bwa.cpp:123:9: warning: ignoring return value of ‘char* fgets(char*, in
fgets((char*) buf, len, fpp);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
src/bwa.cpp:126:9: warning: ignoring return value of ‘char* fgets(char*, in
fgets((char*) buf, len, fpp);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
src/bwa.cpp:129:10: warning: ignoring return value of ‘char* fgets(char*, i
fgets((char*) buf, len, fpp);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
src/bwa.cpp:131:10: warning: ignoring return value of ‘char* fgets(char*, i
fgets((char*) buf, len, fpp);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAItra.cpp -o src/bwamem_extra.o
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAIcpp -o src/bwtbuild.o
src/bwtbuild.cpp: In function ‘int build_index(const char*)’:
src/bwtbuild.cpp:679:64: warning: format ‘%ld’ expects argument of type ‘lo
fprintf(stderr, "init ticks = %ld\n", __rdtsc() - startTick);
~~~~~~~~~~~~~~~~~~~~~^
src/bwtbuild.cpp:711:70: warning: format ‘%ld’ expects argument of type ‘lo
fprintf(stderr, "binary seq ticks = %ld\n", __rdtsc() - startTick);
~~~~~~~~~~~~~~~~~~~~~^
src/bwtbuild.cpp:718:71: warning: format ‘%ld’ expects argument of type ‘lo
fprintf(stderr, "build index ticks = %ld\n", __rdtsc() - startTick);
~~~~~~~~~~~~~~~~~~~~~^
ar rcs libbwa.a src/fastmap.o src/bwtindex.o src/utils.o src/kthread.o src/ src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa
g++ -c -g -O3 -fpermissive -msse4.1 -DENABLE_PREFETCH -DPAIRED_END=1 -DMAI-o src/main.o
g++ -g -O3 -fpermissive -msse4.1 libbwa.a src/main.o -o bwa-mem2 -lpthread
./libbwa.a(fastmap.o): In function `process(void*, gzFile_s*, gzFile_s*, in
/root/software/bwa-mem2/src/fastmap.cpp:547: undefined reference to `pthrea
/root/software/bwa-mem2/src/fastmap.cpp:547: undefined reference to `pthrea
/root/software/bwa-mem2/src/fastmap.cpp:550: undefined reference to `pthrea
/root/software/bwa-mem2/src/fastmap.cpp:550: undefined reference to `pthrea
/root/software/bwa-mem2/src/fastmap.cpp:547: undefined reference to `pthrea
/root/software/bwa-mem2/src/fastmap.cpp:550: undefined reference to `pthrea
./libbwa.a(fastmap.o): In function `main_mem(int, char**)':
/root/software/bwa-mem2/src/fastmap.cpp:936: undefined reference to `gzopen
/root/software/bwa-mem2/src/fastmap.cpp:956: undefined reference to `gzopen
./libbwa.a(utils.o): In function `err_xzopen_core':
/root/software/bwa-mem2/src/utils.cpp:79: undefined reference to `gzdopen'
/root/software/bwa-mem2/src/utils.cpp:84: undefined reference to `gzopen'
./libbwa.a(utils.o): In function `err_gzread.part.1':
/root/software/bwa-mem2/src/utils.cpp:149: undefined reference to `gzerror'
./libbwa.a(utils.o): In function `err_gzread':
/root/software/bwa-mem2/src/utils.cpp:144: undefined reference to `gzread'
/root/software/bwa-mem2/src/utils.cpp:149: undefined reference to `gzerror'
/root/software/bwa-mem2/src/utils.cpp:144: undefined reference to `gzread'
/root/software/bwa-mem2/src/utils.cpp:144: undefined reference to `gzread'
/root/software/bwa-mem2/src/utils.cpp:144: undefined reference to `gzread'
/root/software/bwa-mem2/src/utils.cpp:144: undefined reference to `gzread'
/root/software/bwa-mem2/src/utils.cpp:144: undefined reference to `gzread'
/root/software/bwa-mem2/src/utils.cpp:149: undefined reference to `gzerror'
/root/software/bwa-mem2/src/utils.cpp:144: undefined reference to `gzread'
./libbwa.a(utils.o): In function `err_gzclose':
/root/software/bwa-mem2/src/utils.cpp:269: undefined reference to `gzclose'
/root/software/bwa-mem2/src/utils.cpp:272: undefined reference to `zError'
./libbwa.a(kthread.o): In function `kt_for(void (*)(void*, int, int, int),
/root/software/bwa-mem2/src/kthread.cpp:120: undefined reference to `pthrea
/root/software/bwa-mem2/src/kthread.cpp:123: undefined reference to `pthrea
collect2: error: ld returned 1 exit status
Makefile:86: recipe for target 'bwa-mem2' failed
make: *** [bwa-mem2] Error 1
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yuk12
commented on May 24, 2024
Your system does not support pthread and gz* libraries, please install them to compile the code. Anyways, the next release will be available very soon.
from bwa-mem2.
yuk12
commented on May 24, 2024
We have a new release. Please try that.
from bwa-mem2.
Related Issues (20)
- Does bwa-mem2 preserve a read order from fastq file? HOT 1
- Precompiled AVX512 binary not working for Zen 4 Genoa HOT 7
- Allocation of 40.69 GB for suffix_array failed. HOT 4
- Mapping quality: bad and normal HOT 1
- Index building error
- Read group tag RG:Z for every read is missing HOT 2
- Question regarding the mismatch penalty -B
- Update paths in bwa-mem2-lisa
- Tag New Release HOT 6
- Difference in mapping quality and alignment for bwa mem2 compared to bwa mem HOT 5
- Is bwa really haplotype aware in non-human?
- error while index building HOT 1
- BWA-MEM2-LISA crashed with code 139 HOT 3
- [Question] How to install bwa-mem2-lisa
- Problems creating index with bwa-mem2 HOT 1
- MacOS M2 chip support
- Segmentation fault with valle-inclan dataset - bwa-mem2 2.2.1 avx512bw HOT 1
- bwa and bwa-mem2 relative indexing memory usage HOT 2
- Segmentation fault using bwa-mem2:2.2.1--hd03093a_5 HOT 7
- Add option to align multiple .fastq files at once? HOT 2
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from bwa-mem2.