vpc-ccg / lordfast Goto Github PK

lordfast --search CH17-157L1.fasta --seq 1-1.fastq -t 8
| Reading Input | 0.00 | XXXXXXXXXXXXXXX | 226.15 | XXXXXXXXXXXXXXX 2500 |
[New Thread 0x7fffbfe01700 (LWP 32000)]
[New Thread 0x7fffbf600700 (LWP 32001)]
[New Thread 0x7fffbedff700 (LWP 32002)]
[New Thread 0x7fffbe5fe700 (LWP 32003)]
[New Thread 0x7fffbddfd700 (LWP 32004)]
[New Thread 0x7fffbd5fc700 (LWP 32005)]

Thread 2 "lordfast" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffbfe01700 (LWP 32000)]
0x0000000000408bbb in findTopWins (chunk_overlap=76, seeds=0x11dc260, isRev=0, readIdx=1, id=0) at src/LordFAST.cpp:465
465 if(_pf_refWin_cnt[id][winId].readIdx == readIdx)
(gdb) p readIdx
$1 = 1
(gdb) p _pf_refWin_cnt[id][winId]
Cannot access memory at address 0x7ffff86c0ad0

after generating SAM with lordfast, trying to convert to BAM:

[W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
....

25479 272 22816 0 50 54M * 0 0 TATATCGATATCTACACTCTAGATGCTCATGCTAGTCTCACAGCGACAGCTCAT * AS:i:0
12838 272 47754 0 50 60M * 0 0 CGAGTGATATGCAGTGAGCGAGATCACGCACTGCACAGCTGAGCAGAGCAGACTCATCTC * AS:i:0

and so on. Are you reporting map location 0-based? SAM defines it as 1-based; BAM as 0-based

At the moment SEQ_MAX_LENGTH is hard coded! (50000)
This will cause problems for longer reads, for example for Nanopore data.
Choose SEQ_MAX_LENGTH based on the longest read in each chunk.

Check how changes in bandwidth might change the sensitivity and specificity!

one of these cause a crash. Probably the .gz one, or fasta, or both:

cmdline (reads10.fasta is just 10 reads)

lordfast --search hg19/hg19.fasta --seq /mnt/storage1/projects/giab/pacbio/NA12878_PacBio_MtSinai/reads10.fasta -t 32

......
| Reading Input | 0.00 | XXXXXXXXXXXXXXX | 1466.70 | XXXXXXXXXXXXXXX 9 |
Floating point exception (core dumped)

Check if using LIS instead of CLASP will increase the speed.
I should be careful that the resulting subsequence of anchors might overlap, so I need to modify the extension part a bit!

Hi,
I am getting this bug while trying to compile lordfast.

relocation R_X86_64_32 against symbol `_binary_HELP_start' can not be used when making a PIE object; recompile with -fPIC

cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o stringutils.o stringutils.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o mathematics.o mathematics.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o memman.o memman.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o fileio.o fileio.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o debug.o debug.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o info.o info.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o stack.o stack.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o sort.o sort.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o list.o list.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o vtprogressbar.o vtprogressbar.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o queue.o queue.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o manopt.o manopt.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o sltypes.o sltypes.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o slchain.o slchain.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o bintree.o bintree.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o rangetree.o rangetree.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o vebtree.o vebtree.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o container.o container.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o vstack.o vstack.c
cc -w -pedantic -std=c99 -O3 -DPROG3NFO -DDBGLEVEL=0   -c -o vqueue.o vqueue.c
make[1]: Leaving directory '/home/nguinkal/lordfast/lib/clasp'
make[1]: Entering directory '/home/nguinkal/lordfast/lib/bwa'
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o utils.o utils.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o malloc_wrap.o malloc_wrap.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o bntseq.o bntseq.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o bwt_gen.o bwt_gen.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o bwt.o bwt.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o bwtindex.o bwtindex.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o bwa.o bwa.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o is.o is.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o QSufSort.o QSufSort.c
cc -Wall -Wno-unused-function -Wno-unused-but-set-variable -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS   -c -o ksw.o ksw.c
make[1]: Leaving directory '/home/nguinkal/lordfast/lib/bwa'
g++ -w -fno-pic -DPROG_VERSION=\"0.0.9\" -Ilib/clasp -Ilib/bwa -Ilib/edlib -O2 -DVERBOSITY=0   -c -o src/baseFAST.o src/baseFAST.cpp
g++ -w -fno-pic -DPROG_VERSION=\"0.0.9\" -Ilib/clasp -Ilib/bwa -Ilib/edlib -O2 -DVERBOSITY=0   -c -o src/Common.o src/Common.cpp
g++ -w -fno-pic -DPROG_VERSION=\"0.0.9\" -Ilib/clasp -Ilib/bwa -Ilib/edlib -O2 -DVERBOSITY=0   -c -o src/CommandLineParser.o src/CommandLineParser.cpp
g++ -w -fno-pic -DPROG_VERSION=\"0.0.9\" -Ilib/clasp -Ilib/bwa -Ilib/edlib -O2 -DVERBOSITY=0   -c -o src/Reads.o src/Reads.cpp
g++ -w -fno-pic -DPROG_VERSION=\"0.0.9\" -Ilib/clasp -Ilib/bwa -Ilib/edlib -O2 -DVERBOSITY=0   -c -o src/BWT.o src/BWT.cpp
g++ -w -fno-pic -DPROG_VERSION=\"0.0.9\" -Ilib/clasp -Ilib/bwa -Ilib/edlib -O2 -DVERBOSITY=0   -c -o src/LordFAST.o src/LordFAST.cpp
g++ -w -fno-pic -DPROG_VERSION=\"0.0.9\" -Ilib/clasp -Ilib/bwa -Ilib/edlib -O2 -DVERBOSITY=0   -c -o src/Chain.o src/Chain.cpp
g++ -w -fno-pic -DPROG_VERSION=\"0.0.9\" -Ilib/clasp -Ilib/bwa -Ilib/edlib -O2 -DVERBOSITY=0   -c -o lib/edlib/edlib.o lib/edlib/edlib.cpp
g++ -w src/baseFAST.o src/Common.o src/CommandLineParser.o src/Reads.o src/BWT.o src/LordFAST.o src/Chain.o lib/edlib/edlib.o HELP.o  lib/bwa/*.o lib/clasp/*.o -o lordfast  -lz -lpthread
/usr/bin/x86_64-linux-gnu-ld: src/baseFAST.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: src/Common.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: src/CommandLineParser.o: relocation R_X86_64_32 against symbol `_binary_HELP_start' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: src/Reads.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: src/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/x86_64-linux-gnu-ld: src/LordFAST.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: src/Chain.o: relocation R_X86_64_32 against symbol `cmp_slmatch_qsort' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: lib/edlib/edlib.o: relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status ```

Do you know if the bam output is compatible with the pacbio arrow tool which is a bit picky about the format.

setting RG tags while mapping would be good to have.

When aligning FASTA sequences, erroneous characters are added at the end of a sam line:

test
CATTCCCTCAATTAGATTTAAGATTCCTTTCCATTAACATCTGTGCAAATCTAAGCAACCCTGCTGTTGGCCACATGGATTACATGTGCTGCAAAATCAACCCCAAGAAATCCTATTGCTCAACAGGAAGCAGTAACCCCTGCTTCCATAGAGAAGCACACTAGAACTTGCTTCAAGTGGACAAATATTTCACCGAAACAATTCAAGCACCTTTTCAGACTTTTCGAGCTCTACGAAATGGTCCTCTTGATTAAGCATGTGTGTGCCCCCAGTCCCATGCCATAGACTCGACTCATTCATTAAACCTACCTAAGCTGAAACCGGCTGGGGCTGAGTCTTAGATATCTCCTAGCTTCTGCCAAAAGATTGAGCTTCAGCCAGCATGCAGCACTGATCCCAGACTTGGAGCCGAGCAAGTGATCAACTGCATAGATAAGACATCTAGGCACATAGGAACCACTCTACAAAAAATACATAAAATAACTGGCGTGTGCACGGCCGTACTATATTCGCGAGCTAAGTGGAGGATCGCTTTGTGATTAAGGCTCAATACTGTCACACACTTATCCAGCCTCATGACAACTAATGCGGAGCAGTCTCAAAACAAAACAAAACAAAACCACAAAACCTGCAGCCTGCACACTTACTGGTAGGCTGCTCAAGCAGCACTTACAGGTGACAATATAGTTATTTTAATCTAGGGTGTTGTATTCTCAAGTAAAAATTCACTTCTCCTCCTTTGAAGTAGATGTGACTGATGATCTGGCCAAGAATGTGACCCGAAAAGACCGGACCTCCAAGGGAGCTTAAAAGCCAGTGACAATATCACTGATCCTCTGCTTCAATCATCCGTAGAACCCAGTCAGGAGGAACTCCACGCCTGGATCTGATTAGGACCCTGTTAGATCAAAAATATAAGTTTTAACAAGAAAGGACGTTCTATTGCAACATAACTAGTCCTATTGACTGATAACCCAGTGTAATATATCATGGATTTTCTAGCCAAGTTCCATGTAGATGACTTTGGGGTTATTTATTGCTTCTGGACCATCCGTGCATGCAAGATTTAAATTGGCTCGTAGCCTTTACCCTAACACCAGCACACCCATCCGCAAGTTGACACAAAACCTCAACAGTCGATCCACTTATTGAGGTCCTAAGAGTCAAATCTGAGACAGAATCAATATGGTTTAGGGCTGGAGAAAGGAATGGCGAGTTAGTGTTAATGTGTACATATTACAGTTTGCAAGAATTAAAAGAGTTCTAATGGATGCTGTGTGATTGTTCACATCATGTGAGGTAGTCACGAACATCATAAATGGTTCATATTAATTATGATTCTTTGCCAAATTTTGAAATGAAAAAATGTTTCATACATTGCCAATCCCTGGAAAGCATAATCGCCCTGTGAATATTTGTTTATCGATGCGACCATTCAATTGTAAAATATTGAAAACGTTGGCTAGGCTCACCATGCTTTTGCCATGAAGTTAGAATCTCATCTCTCTATAATATTTTTATCCACTCAATTTAGGCCAGGATCAATAGGACATTAACTTTGACTAGAAAAACCTGTCTATGACCAAAACTGTGTGATAGAATACATCGTAAAAACCTTACCTGTTTAAGCTTACATCTAAACAGAGCACAGTAGACTCCACTTGGATCATTTTCCTGAAACCTACTGTTTTTCATGCTGGTTTCTGGCAGTTAAGGTGCGTCTAAAGATGTTGATGCAAAAATGGAATGACCAGGACACACAGGATTTTTCCCAAATGAAGAAACTCAAACCTGCAGGCATCCTGCTGCGGAAGAGATCTCACTCGAATGCATCTGAGGATCTCTCCAACCCTGAGGATAAATAGGCTAAAAGGGCCAAATGGTGATTGGCCGCCTGACAATTGATACTCCAATGCTCGTGACGGCTAAATGTGATGGCCTGCTTGACATGAATCCAGCCGACTGGCCAAAGTATTGGCTCTGCCTTGACCATTGAACCATGCTCGACCGAGGCAGCAGAGGCTTCTACACCCACCTCCACACATACCTGCCAAGTCACTCTAACCCTCTTCATAGTAAGGGCCCCATCTATGCTCACCCTTTTCCATAATGACCCTGCCAGATTGCCACATCTAAAACAAGGTGCTGTTACTGCTGTATGGACACTTCATCTCAAGTGAGGGCCCGCTCACATGATTGCAGGTTCTTTCTCTGGCCTCAAAACATCTCCAGTTGAGGCGAACCTGCTTCCTCCCAAAGCCCCAACTAGGCATGAACAGAATTATCCTCCCTTCTGTTCTCAGGCCTAGAATTAACTAATCCTCTCCACAAAGTAGGTTTATTTCAAAGCTGTTATCAGCGCTCTTCTGCCATCTGCTCTTGAGTTTGCTGGGAACACCCACGTGCTTGAGCTGCCTGTCACCTCGCCCCATACTTCTCCCCCACACTCAAACACATCTGCATCGGCACCTCCACCTCCAGTTCCCCACAGTGATCCATCCTTGCCGCTCCAGGCCAGCCCTTGGGAGTGCGCTTCAATATGCACTAGTTCAGCATCTTTAGCACCCATGTCCATGGGTTTTCATTTATTCAATTATAAATGTTTAAACTCTCCGTCCTGGAAAAAAAAAAAGTCCAATAACCATCTCCCTCTTTAGCTTAAGTCACTGTAATCTCCTTTCCATTTTTACTCATGTCCCAGGTTTAAACAGTATCCACACACCCTCAAAATTTCTGTCTCCACCTAGGAATCTAGAATGTGATGTTATTTGGAAAATAGTGTTGAGAGTAATTGTTAGATGGACCTAGTCCACTATACTGTGCGGTGCCTTAAGAAAAGAATAAGGAACGCAGAGCACACCAGAGATACCATGGCTGATGTGGCGAAACTGGGTTGTATCTACAGAATGAATCATGTGGCAGGTAAACCCAGAATACGAACGAAAGCATGGAGCAGATCTTCCAGCATTCCAAGAGATCAGTGTTGGCCACACCTCGTTTGAACTCATCTCAAAACGTGAGAAAAAATTTTCTGTGTTAAACAAGACCCATTTGTTAATTTGGTGACAGCAAACCTGAACTGAATACCCTTAACACACCGTTCTTTGGTTCCAAGACTTTCGTGTATGACTGCGAAGCCAAATCCATTTATGCCCTCTGGAGCTCGTCAACATTATTCTTATTGAGCCTTCCCCACATACTCTCGCCTCCTCCATGCTTCAATCACGGCCACTCCCGCATACGGAGCCTGTTCATCACACTTTCACTCTGTCATCTCCACGCAACTCATCCAATTAACCACTCTCCCCACACCATGCTTGATGATCCCCAAGCCCTCTGGCCAAGCCCTTCCCCTGATCTTACTTGAGTCCCCACTGCCATCACTCACTATCTGTCACAGCACTCAAAAACACACCAAAATGGAACATGGTCTAAACTCTTCCCAAATAACCTGCTTTCTCCTGTACCTGCAATCAATGAGAGGCTTCACTTCACAAGGATAAGCCATAACCTGCAACTCTGGCTTCTCGCACCTTGGCCGTGGTCATGATCAAAGACTCTGCCATAAGGTTTGGGAATGTACTCGCATCTGCGCACTGCTCAGCCAGCCTCTCATTTGTGCTGGGAGACTCCCTACATCCTAGACTTTCATTGCTGCTCTTGTGAGCACTTCTTATAACCACCTTGTTACCATTCCCTGCTTCGAATGCTTCAGGTCTGTCACCTGCAGATATCCTTAATCCCTCACTTGATTAACTAACGCTTGTTAGCATCTGGCTTCAGGAGTTTAGATTGGAGGGCTCTGCATCCACCCAGGACCTACCACATACTTGGCGTGGCCTGGCAACAACTTACTCTCTCTGTCTCAGATTCCCACCGAAAGGGATAATCATAGTACTACTCATAGAGTTTTGAAAATAATGATCGAATATGTCAGAGTACGCGAACTGTCAGCATTCGACAGGCATTATTAATAATAACTGCTGTCTGTATTATACTTCCCACATCTGTCCATTCCCAGTGCGTTGTTCCAGCCATCAGAACACCCTTCATCTAGAAGAAACAAAAAGCCTCTACCTGTTCCTCTGCTCTTGCCTTGACACCACTGTCTTGTGAATACTTATCCAACCACCTCTCACCATGCTCCTTAAACATACTTCGACTCATCTTTTCGACCTAGTACTTCTCCCCTGAGAAAGCAGCTCTCTGAGCCTTCGTAGGCGCTGTTTCTCACCTATTTGGCAGCACAGATCACACTCATATAAGACTCTCGCCCCGCCATCTTCCGAGTTTGCTGTATTGATATAGTGATCAGCCACGTGGCACTCAGCCTAACAATAGAAAGCAGGTCAATAAAGGCTGTATAATTAGAATGATAAGGCATAAAAGAGGAGCGGGTACAATAGTCCAGGCTGCTGGGATAGTCCTGGTTTAGGCCATGCCTGGATAGTAATACTATACAACACCCTCTTCCACTGTAAAATATTCTCCTTTGACAATACATTAAAGCTCCTGTATAGAAGCTGTGTCTCACCATCAGGCCCAATTTCTCTTGCTTAACAGCATTTTAGAATACCTAACAATTTTTAATGGATTGGATAGCAATAGAACCGCAAAACGAATCAAAAAAACCAATTAAACCTAATTCAAGCTAAGGAAAAATGAAGCAGATTTTAAAATACTAACATAATTTATTTGGCAGTATTGATGTGTAAACTATGTCTACACTTCTGGCAAAGAGTGAGTAAACAGAGACCAAAATTACTTCTGCCTAAAACACAAAATATACTGGAACAAAATATATGAAACATGGTCCTCAAGAACAAAGGAATCAATCACTGAATCAAGCACAAGGGCAGTGATCCTCA

@pg ID:pacfast PN:pacfast VN:0.1.0 CL:/home/cmb-16/mjc/shared/software_packages/lordfast/lordfast --search hg38.fa --seq test.fasta
Reading input... loaded 1 reads in 0.00 seconds (0.00 CPU seconds)
mapping... test 0 chr9 97748 32 2M1I13M2D17M2D7M1D1M2D1M1D22M1D2M1D13M1D7M1D36M1I4M1D6M1D18M1D7M2D6M1D1M2D15M1D10M2D4M1D1M1D4M1D8M1D1M1D7M1D6M1D6M1D1M1D2M1D3M1I10M1I11M2D1M1D3M1D3M1D6M1D4M1D13M2D5M1D1M1D11M1D2M1D3M1D2M1D4M1D2M1D8M1D4M3D4M1D1M1D6M1D4M1D1M1D4M1I9M1D4M1D13M1D2M1D4M1D4M1D4M2D2M3D2M1D1M1D6M1D4M1D2M1D2M1D5M1D6M1D4M1I2M1D4M2D2M1D1M1D1M2D5M1D1M1D8M1D5M1D3M1D2M2D1M1D12M1D10M1D6M1D4M1D2M1D5M1D2M1D3M2D2M1D1M2D5M1D1M1I3M1D2M1D6M1D10M1D4M3D2M1D1M1D6M1D5M2D6M3D3M1D3M1D2M1D8M1D7M1D8M1D4M2D7M1D4M1D18M1I18M1D3M2D12M1D4M2D1M1D10M1D1M2D10M3D3M1D2M1D2M1D5M1D3M2D5M1D3M1D1M2D1M1D5M1D1M1D3M1D16M1D1M1D5M1D8M1D7M1D2M1D2M2D2M2D12M1D2M1D7M1I5M1D4M1D4M1D2M1D4M1D8M1D11M1D5M2D12M4D14M1I6M1D5M1D6M1D8M1D2M2D8M2D7M1D3M2D1M1D2M1D22M1D3M1D1M1I5M1D11M2I1M1I1M1I11M1D13M1I1M1D3M1D1M1D8M1D1M1D6M1D5M1D5M1D2M1D4M1D1M1D2M1D1M3D1M1D3M1D2M1D3M1D20M1D2M1D1M1D1M3D7M1D6M1D7M1D6M1I3M1D2M1D13M2D2M1D9M1D5M1D4M1I7M2D2M1D1M1D5M2D2M1D9M1D3M1D9M1D5M1D4M1D2M1D7M1D2M1D2M1D8M2D4M1D1M1D6M1D1M1D4M1D4M1D4M1D3M1D2M1D15M1D12M1D9M1D4M1I16M1I7M1D2M1D2M1D8M1D7M1D5M1D3M4D3M1D1M1D2M1D4M1D2M1D2M2D1M1D3M1D10M3D5M2D3M2D2M1D1M1D8M1D6M1D4M1D2M1D6M3D6M1D13M2D3M1D18M1D2M1D1M1D2M1D1M2D4M1I3M1D5M2D1M1D6M1D18M1D2M1D4M1D8M1D3M1D4M1D10M1D5M1D3M1D18M1D1M1D1M1I9M1D9M1D4M1D20M1D2M1D3M2D5M1D9M1D2M2D8M1D3M1D7M1D7M1D7M1D2M1D8M1D5M1D6M1D6M1D6M1D1M1D1M1D15M2D10M1D4M1D17M1D13M1I6M1I12M2D1M1D3M1D3M1I4M1D1M1D9M1D1M1D3M1D2M1I2M1D3M1D2M1D5M1D4M1D5M1I2M1I6M1D4M1I2M1D12M1D2M1D4M2D12M2D4M2D5M1D10M1D5M1D3M1D5M1D4M1I5M1D5M2D7M1D5M2D2M1D14M1D1M1D2M1D2M1D3M1D6M1I6M1I6M1I3M1D2M2D1M1D6M1D4M1D3M1D5M1D1M1D3M1D1M1D1M1D4M1D3M1D2M1D2M1D5M2D2M1D3M1D1M1D1M1D11M1D8M1D6M1D1M1D6M1D17M1D5M1D14M1D2M1D2M1D3M1D4M1D6M1D4M1D1M1D2M1D6M1D1M1D2M3D5M1D6M1D3M1D2M1D5M1D2M1D19M1D1M1I13M1D4M1D2M2D2M1D1M1D2M1D1M2D2M1D1M1I29M1D10M1D12M1D5M1D3M1D12M1D1M1D7M1D6M1D7M1D9M1I2M1I12M1D16M1I9M1D5M1D1M1D6M1D3M1I6M2D1M1D14M2D13M1D6M1D10M2D4M1D4M1D22M1I3M1D2M1D7M1D1M1D1M1D8M1D6M1D7M1D2M1D7M1D1M1D1M1D5M3D31M1D1M3D3M1D2M1D9M2D9M1D8M1D1M1D3M1I10M2D5M1D7M1D1M1D5M1D5M1D1M1D1M1D5M1D17M1D2M1D14M1D15M1D2M1D3M1D10M1D5M1D22M1D1M1D2M2D4M2D19M1D4M1D9M1D11M1D2M1D4M1D13M1I28M1D3M1D4M1I1M1I9M1D9M1D1M1I11M1I3M2D1M1D4M1D3M1D7M1D4M1D1M1D6M1D1M1D10M1D4M1D2M1D5M1D5M1I3M1D7M1D3M1D9M1D5M1D7M1D1M2D5M1D10M1D2M1D8M1D1M2D10M1D1M2D7M2D4M2D7M1I6M1D5M1I6M1D4M1D12M1D5M1D5M1D4M1D8M1D1M1D5M1I3M1D10M1D5M1D1M1D4M1D1M1D5M1D6M1D13M1D4M1D8M1D1M1D2M1D5M2D7M1I13M1D3M1D7M2D5M1D2M1D1M1D2M1D6M2D1M1D3M1D10M2D14M1D5M1D11M1D1M1D2M1D2M2D1M1D2M1D13M1D4M2D3M1D4M1D7M1D4M1D5M1D7M1D4M1D10M1D5M2D4M2D7M1D11M1D4M1D2M1D2M2D8M1D2M1D3M1D1M2D7M1D3M1D6M1D4M1D12M1I3M1D6M1D2M1D5M1D5M1I5M1D18M1D5M1D2M1I7M2D3M1I4M1D4M1D10M1I2M4D2M1D1M2D1M1D2M1D3M2D2M1D2M1I3M1D5M1D7M1D4M2D1M1D9M2D9M1D2M1D1M1D2M1D11M1D8M2D8M1D7M1D17M1D6M1D3M3D10M1D5M1D5M1D2M1D2M1D6M4D5M1D13M1D4M1D1M1D4M1D8M1D6M1D6M1D6M1D1M1D2M1D5M2D3M1D3M1D5M1D4M1D8M2D1M1D1M2D1M1D5M1D2M1D1M1D6M1D3M1D5M1I2M1I10M1I10M1I8M1D6M1I10M2D1M2D8M1D18M1D1M2D1M1D2M1D10M1D2M1D2M1D2M1D3M2D7M1D5M1D6M1I5M1D4M1I12M1D20M1D11M1D1M1D22M2D7M1D3M1D5M1D15M1D1M1D9M1D4M1D4M2D3M1D13M1D3M1D10M1D3M1D3M1D2M1D2M1D13M1D11M1D6M2D1M1D5M1D3M1D3M1D2M1D5M2I15M2D4M1D2M1D3M1D2M1D2M1D3M1D2M2D2M2D7M2D6M1D10M2D6M1D15M1D4M1D14M2D3M1I8M1D1M1D6M1D6M1D9M1D8M1I1M1I6M1D2M1I15M1D2M1D7M1D1M1D25M1D6M1D5M1I8M1D3M1D5M1D5M1D1M2D12M1D6M1D3M1I9M1D3M1I16M1D3M1D4M1D1M1D2M2D4M2D1M1D1M1D1M1D3M1D9M1D19M1D6M2D4M1I14M1I2M1D4M1I10M1D13M1D8M1D4M1D1M1D4M1D5M1D3M1D4M1I1M1D1M1I8M1D2M1D4M1D6M1D26M2D4M1I3M1I4M1D4M1I20M1D4M1D3M1I8M1D11M1D6M1D2M3D1M1D3M1D3M1I6M1D1M1D6M2D14M1D5M1D10M1D13M1D3M1D4M1D1M1D5M1D3M1D4M1I4M1D10M1D2M1D2M1D3M1D4M2D13M1D3M1D3M1D6M1D2M1D3M1D2M1D2M1I17M3D4M1D2M1D2M1D2M1D1M1D6M1I5M1D8M2D10M2D2M1D6M1D16M1I2M1D5M1I18M1D3M1D9M1D5M1I8M1I15M1D12M1D8M1D12M1D9M1D3M1D15M * 0 0 CATTCCCTCAATTAGATTTAAGATTCCTTTCCATTAACATCTGTGCAAATCTAAGCAACCCTGCTGTTGGCCACATGGATTACATGTGCTGCAAAATCAACCCCAAGAAATCCTATTGCTCAACAGGAAGCAGTAACCCCTGCTTCCATAGAGAAGCACACTAGAACTTGCTTCAAGTGGACAAATATTTCACCGAAACAATTCAAGCACCTTTTCAGACTTTTCGAGCTCTACGAAATGGTCCTCTTGATTAAGCATGTGTGTGCCCCCAGTCCCATGCCATAGACTCGACTCATTCATTAAACCTACCTAAGCTGAAACCGGCTGGGGCTGAGTCTTAGATATCTCCTAGCTTCTGCCAAAAGATTGAGCTTCAGCCAGCATGCAGCACTGATCCCAGACTTGGAGCCGAGCAAGTGATCAACTGCATAGATAAGACATCTAGGCACATAGGAACCACTCTACAAAAAATACATAAAATAACTGGCGTGTGCACGGCCGTACTATATTCGCGAGCTAAGTGGAGGATCGCTTTGTGATTAAGGCTCAATACTGTCACACACTTATCCAGCCTCATGACAACTAATGCGGAGCAGTCTCAAAACAAAACAAAACAAAACCACAAAACCTGCAGCCTGCACACTTACTGGTAGGCTGCTCAAGCAGCACTTACAGGTGACAATATAGTTATTTTAATCTAGGGTGTTGTATTCTCAAGTAAAAATTCACTTCTCCTCCTTTGAAGTAGATGTGACTGATGATCTGGCCAAGAATGTGACCCGAAAAGACCGGACCTCCAAGGGAGCTTAAAAGCCAGTGACAATATCACTGATCCTCTGCTTCAATCATCCGTAGAACCCAGTCAGGAGGAACTCCACGCCTGGATCTGATTAGGACCCTGTTAGATCAAAAATATAAGTTTTAACAAGAAAGGACGTTCTATTGCAACATAACTAGTCCTATTGACTGATAACCCAGTGTAATATATCATGGATTTTCTAGCCAAGTTCCATGTAGATGACTTTGGGGTTATTTATTGCTTCTGGACCATCCGTGCATGCAAGATTTAAATTGGCTCGTAGCCTTTACCCTAACACCAGCACACCCATCCGCAAGTTGACACAAAACCTCAACAGTCGATCCACTTATTGAGGTCCTAAGAGTCAAATCTGAGACAGAATCAATATGGTTTAGGGCTGGAGAAAGGAATGGCGAGTTAGTGTTAATGTGTACATATTACAGTTTGCAAGAATTAAAAGAGTTCTAATGGATGCTGTGTGATTGTTCACATCATGTGAGGTAGTCACGAACATCATAAATGGTTCATATTAATTATGATTCTTTGCCAAATTTTGAAATGAAAAAATGTTTCATACATTGCCAATCCCTGGAAAGCATAATCGCCCTGTGAATATTTGTTTATCGATGCGACCATTCAATTGTAAAATATTGAAAACGTTGGCTAGGCTCACCATGCTTTTGCCATGAAGTTAGAATCTCATCTCTCTATAATATTTTTATCCACTCAATTTAGGCCAGGATCAATAGGACATTAACTTTGACTAGAAAAACCTGTCTATGACCAAAACTGTGTGATAGAATACATCGTAAAAACCTTACCTGTTTAAGCTTACATCTAAACAGAGCACAGTAGACTCCACTTGGATCATTTTCCTGAAACCTACTGTTTTTCATGCTGGTTTCTGGCAGTTAAGGTGCGTCTAAAGATGTTGATGCAAAAATGGAATGACCAGGACACACAGGATTTTTCCCAAATGAAGAAACTCAAACCTGCAGGCATCCTGCTGCGGAAGAGATCTCACTCGAATGCATCTGAGGATCTCTCCAACCCTGAGGATAAATAGGCTAAAAGGGCCAAATGGTGATTGGCCGCCTGACAATTGATACTCCAATGCTCGTGACGGCTAAATGTGATGGCCTGCTTGACATGAATCCAGCCGACTGGCCAAAGTATTGGCTCTGCCTTGACCATTGAACCATGCTCGACCGAGGCAGCAGAGGCTTCTACACCCACCTCCACACATACCTGCCAAGTCACTCTAACCCTCTTCATAGTAAGGGCCCCATCTATGCTCACCCTTTTCCATAATGACCCTGCCAGATTGCCACATCTAAAACAAGGTGCTGTTACTGCTGTATGGACACTTCATCTCAAGTGAGGGCCCGCTCACATGATTGCAGGTTCTTTCTCTGGCCTCAAAACATCTCCAGTTGAGGCGAACCTGCTTCCTCCCAAAGCCCCAACTAGGCATGAACAGAATTATCCTCCCTTCTGTTCTCAGGCCTAGAATTAACTAATCCTCTCCACAAAGTAGGTTTATTTCAAAGCTGTTATCAGCGCTCTTCTGCCATCTGCTCTTGAGTTTGCTGGGAACACCCACGTGCTTGAGCTGCCTGTCACCTCGCCCCATACTTCTCCCCCACACTCAAACACATCTGCATCGGCACCTCCACCTCCAGTTCCCCACAGTGATCCATCCTTGCCGCTCCAGGCCAGCCCTTGGGAGTGCGCTTCAATATGCACTAGTTCAGCATCTTTAGCACCCATGTCCATGGGTTTTCATTTATTCAATTATAAATGTTTAAACTCTCCGTCCTGGAAAAAAAAAAAGTCCAATAACCATCTCCCTCTTTAGCTTAAGTCACTGTAATCTCCTTTCCATTTTTACTCATGTCCCAGGTTTAAACAGTATCCACACACCCTCAAAATTTCTGTCTCCACCTAGGAATCTAGAATGTGATGTTATTTGGAAAATAGTGTTGAGAGTAATTGTTAGATGGACCTAGTCCACTATACTGTGCGGTGCCTTAAGAAAAGAATAAGGAACGCAGAGCACACCAGAGATACCATGGCTGATGTGGCGAAACTGGGTTGTATCTACAGAATGAATCATGTGGCAGGTAAACCCAGAATACGAACGAAAGCATGGAGCAGATCTTCCAGCATTCCAAGAGATCAGTGTTGGCCACACCTCGTTTGAACTCATCTCAAAACGTGAGAAAAAATTTTCTGTGTTAAACAAGACCCATTTGTTAATTTGGTGACAGCAAACCTGAACTGAATACCCTTAACACACCGTTCTTTGGTTCCAAGACTTTCGTGTATGACTGCGAAGCCAAATCCATTTATGCCCTCTGGAGCTCGTCAACATTATTCTTATTGAGCCTTCCCCACATACTCTCGCCTCCTCCATGCTTCAATCACGGCCACTCCCGCATACGGAGCCTGTTCATCACACTTTCACTCTGTCATCTCCACGCAACTCATCCAATTAACCACTCTCCCCACACCATGCTTGATGATCCCCAAGCCCTCTGGCCAAGCCCTTCCCCTGATCTTACTTGAGTCCCCACTGCCATCACTCACTATCTGTCACAGCACTCAAAAACACACCAAAATGGAACATGGTCTAAACTCTTCCCAAATAACCTGCTTTCTCCTGTACCTGCAATCAATGAGAGGCTTCACTTCACAAGGATAAGCCATAACCTGCAACTCTGGCTTCTCGCACCTTGGCCGTGGTCATGATCAAAGACTCTGCCATAAGGTTTGGGAATGTACTCGCATCTGCGCACTGCTCAGCCAGCCTCTCATTTGTGCTGGGAGACTCCCTACATCCTAGACTTTCATTGCTGCTCTTGTGAGCACTTCTTATAACCACCTTGTTACCATTCCCTGCTTCGAATGCTTCAGGTCTGTCACCTGCAGATATCCTTAATCCCTCACTTGATTAACTAACGCTTGTTAGCATCTGGCTTCAGGAGTTTAGATTGGAGGGCTCTGCATCCACCCAGGACCTACCACATACTTGGCGTGGCCTGGCAACAACTTACTCTCTCTGTCTCAGATTCCCACCGAAAGGGATAATCATAGTACTACTCATAGAGTTTTGAAAATAATGATCGAATATGTCAGAGTACGCGAACTGTCAGCATTCGACAGGCATTATTAATAATAACTGCTGTCTGTATTATACTTCCCACATCTGTCCATTCCCAGTGCGTTGTTCCAGCCATCAGAACACCCTTCATCTAGAAGAAACAAAAAGCCTCTACCTGTTCCTCTGCTCTTGCCTTGACACCACTGTCTTGTGAATACTTATCCAACCACCTCTCACCATGCTCCTTAAACATACTTCGACTCATCTTTTCGACCTAGTACTTCTCCCCTGAGAAAGCAGCTCTCTGAGCCTTCGTAGGCGCTGTTTCTCACCTATTTGGCAGCACAGATCACACTCATATAAGACTCTCGCCCCGCCATCTTCCGAGTTTGCTGTATTGATATAGTGATCAGCCACGTGGCACTCAGCCTAACAATAGAAAGCAGGTCAATAAAGGCTGTATAATTAGAATGATAAGGCATAAAAGAGGAGCGGGTACAATAGTCCAGGCTGCTGGGATAGTCCTGGTTTAGGCCATGCCTGGATAGTAATACTATACAACACCCTCTTCCACTGTAAAATATTCTCCTTTGACAATACATTAAAGCTCCTGTATAGAAGCTGTGTCTCACCATCAGGCCCAATTTCTCTTGCTTAACAGCATTTTAGAATACCTAACAATTTTTAATGGATTGGATAGCAATAGAACCGCAAAACGAATCAAAAAAACCAATTAAACCTAATTCAAGCTAAGGAAAAATGAAGCAGATTTTAAAATACTAACATAATTTATTTGGCAGTATTGATGTGTAAACTATGTCTACACTTCTGGCAAAGAGTGAGTAAACAGAGACCAAAATTACTTCTGCCTAAAACACAAAATATACTGGAACAAAATATATGAAACATGGTCCTCAAGAACAAAGGAATCAATCACTGAATCAAGCACAAGGGCAGTGATCCTCA * AS:i:3718 XS:i:0 NM:i:1149 MD:Z:15^TG17^CT7^C1^TG1^G16G5^T2^T13^G0G6^T1C38^T6^G18^C3G3^GT6^T1^GT11T3^G10^TT4^C1^G4^T8^G1^T7^T6^C6^A1^G2^G6T11G5^TG1^G3^T3^G6^T4^T13^AG5^A1^C11^T2^A3^G2^C4^G2^T8^T4^CCT4^T1^G6^T4^C1^C13^G4^T4A8^T2^G4^G4^G4^TC2^GCC2^T1^A6^C4^T2^G2^G5^G6^G6^T4^CC2^G1^G1^TC5^C1^G8^A5^T3^A2^CC1^T12^A4A5^T6^G4^G2^G5^G2^T3^GT2^C1^AC5^A4^G2^G6^G10^G4^GGG1G0^G1^C6^G5^AG4G1^TGA3^C3^G2^C8^G7^G5G2^T4^TG7^C4^A36^C3^CC12^T4^TG1^T10^C1^AG7T2^CAG3^G2^G2^T5^T3^TG5^T3^G1^GG1^T5^T1^C3^G9G6^C1^T5^C8^G7^G2^C2^TG2^TT12^G2^G12^T4^T4^A2^T4^T8^T11^C5^TT12^TTTT8G11^G5^G6^T8^C2^CA8^TG7^A3^TG1^T2^A7G14^G2T0^T3C0C1^C2A1A0T2G0G14^T14^T3^T1^G5G2^T1^C6^G5^T5^T2^G4^T1^T2^A1^TTT1^G3^G2^T3^G10G9^T2^T1^T1^GGG7^T6^T3G3^G4G4^C2^C13^AC2^G9^G5^C11^TG2^C1^T5^AT2^C8A0^T3^T9^T5^A4^G2^T7^A2^G2^G8^AG4^A1^G6^G1^C4^G4^G4^G3^G2^A15^T10G1^G9^T7G18G0^A2^G2^G4G3^G7^G5^A3^GCTT3^G1^C2^T4^T2^A2^CA1^G3^A7G2^GGC5^TT3^TT2^G1^G8^C6^T4^A2^G6^AAA3C2^C1G11^GT3^C9A8^C2^G1^T2^G1^AC2G4^C2G2^GT1^G6^A18^G2^T4^A3G4^T3^G4^G2C7^T5^T2G0^G18^C1^G10^T9^G4^T20^A2^G3^GG5^T9^G2^CC8^G3^C7^G7^T7^C2^T8^T5^A6^T6^T6^G1^T1^A15^GA10^G2A1^T17^T24T6^CT1^G3^T7^G1^T2A6^G1^A3^G4^G3^A2^G5^T4^G1G11^C6^G12^G2^G4^CT12^GG1G2^TA5^T10^T5^G3^T5^T9^A5^TC7^C5^GG2^T14^T1^T2^T2^T3^C21^T2^GG1^C6^G4^T3^T5^C1^T3^C1^A1^T4^T3^T2^T2^G5^GG2^T3^T1^G1^G11^T8^A6^T1^C6^G17^G5^T14^C2^C2^C3^C4^T6^T3A0^G1^G1A0^T6^T1^T2^CTC4T0^T5T0^A3^T2^T5^T2^G19^C14^C4^G2^CC2^T1^C2^A1^GG2^G30^A7G2^A12^T5^G3^C12^T1^T7^T6^G7^T3A19^T1A23^T5^T1^G6^T9^CC1^T3C10^CC10G2^G6^C10^TT4^T4^G25^T2^C7^T1^C1^G8^G6^A7^G2^T7^A1^C1^G5^GGC31^A1^CCC3^C2^G1C7^TG9^G8^A1^C13^CC5^C7^C1^T5^A5^T1^C1^T5^T7A9^C2^T12T1^A15^G2^G3^C10^C5^C22^T1^C2^TT4^CT19^A4^T9^T4G6^A2^T4^C12G18C5A3^C3^T14^T9^C15^GG1^T4^C3^T7^G4^G1^G6^C1^T1A8^G4^G2^T5^T8^G7^G3^G9^G5^A6G0^G1^GG5^T1A5G2^G2^G8^G1^GG10^A1^CC2G4^GT2G1^GC1T11^C4G4T1^G4^G12^T5^T5^C1T2^G5G2^T1^G2C5^A10^T5^T1^T1G2^T1^C5^T6^G5A7^T3T0^T8^A1^T2^G3C1^GG2T12G4^A3^A7^TA5^T2^A1^C2^C6^TT1^C3^T10^TT14^C5^G11^G1^C2^T2^TT1^G2^T9A3^G4^TC3^T4^C7^T2T1^C5^C4C2^T4^G6T3^T5^CT4^TC2A4^G2A8^T4^T2^C2^GG8^C2^C3^T1^CC7^T3^G6^T4^T9A5^G6^T2^C2C2^C10^T18^T5^T3T5^GA7^T4^T12^CTGG2^A1^TT1^C2^C2G0^AA2^T5^A5^T7^T3T0^GG1^T9^GT9^G2^G1^C2^C11^A8^TT8^A6T0^G17^G6^C3^GGC8G1^C5^G2T2^T2^T2^G6^CTCT5^C13^C3A0^G1^C4^G8^T6^G6^G6^T1^C2^T5^CC3^T3^G5^T4^T8^TA1^C1^CC1^C5^G2^A1^C6^C3^A25G9^T16^TT1^AG8^C18^G1^TT1^C2^G10^G2^G2^G2^C3^GC2T4^C5^G1A9^C16^T12G7^G8T2^A1^T22^TG7^C3^G5^T15^G1^C9^T4^T4^AT3^G13^C3^C10^G3^T3^G2^T2^A3G9^T8C2^G6^GT1^C5^G3^T1A1^T2^G2C6T10^TG4^T1A0^G3^T2^C2^T3^C2^TC2^TT4A2^GC6^T10^TT6^G10T4^C4^T8A5^AA11^G1^T2C3^G6^G9^A15^C5C11^T2^C7^C1^G1G23^T6^A4C8^C2T0^C5^C5^T1^AC12^A6^T2G7C1^A19^G3^T4^A1^G2^CA4^CT1^T1^T1^T3^T7T1^A17C1^T6^GT20^G14^C13^G2G5^A4^T1^T4^A5^T3^T5^T9^A2^T4^C6^C26^GT11^T17T6^C4^A11^G11^T3G2^A2^CTA1^G3^T9^A1^T6^CT14^T5^T10^T13^C2T0^G2C1^A1^C5^A3^G8^G8A1^T2^C2^T3^A4^TT8A4^G3^T3^C3A1A0^G2^T3^T2^T19^TTT4^G2^G2^T2^A1^T1A6G2^T8^TT10^TG2^T1G4^T11C6^G23^T3^A9^A28^T4C7^C8^G12^G9^T3^A15

Hi folks - I am unable to get lordfast to work; compiling from source (git master) or installating from bioconda leads to a quick segfault - this is seen on both Centos and macOS. Any thoughts as to what I may be doing wrong? TIA

 ./lordfast/lordfast --search Homo_sapiens.GRCh37.75.dna.chromosome.20.fa --seq clive.chr20.fastq
[NOTE] number of threads: 1
[NOTE] (bwt_load) loading the index...

[NOTE] (bwt_load) index was loaded in 0.34 seconds (0.34 CPU seconds)
@HD     VN:1.5  SO:unsorted
@SQ     SN:20   LN:63025520
@PG     ID:lordfast     PN:lordfast     VN:0.0.10       CL:./lordfast/lordfast --search Homo_sapiens.GRCh37.75.dna.chromosome.20.fa --seq clive.chr20.fastq
Reading input... loaded 1837 reads in 0.16 seconds (0.16 CPU seconds)
        mapping... Segmentation fault

The function getLocs_extend_whole_step() does not check if there are at least minMatch bases left for seed extraction.
A bug when the read length is smaller than 1014 bases.

Soft-clipping is already implemented for ksw library.
For edlib library, the prefix (SHW) mode aligns the whole query to the reference so there shouldn't be much clipping.
However, sometimes there are a few insertions at the beginning of the CIGAR string.
This should be soft-clipping actually.

In general, the memory usage should be around 5.7 GB for the human.
However, when mapping a big data set the memory usage is higher.
Check why and fix it.