Hello! in the dragmap folder I tried: build/release/dragen-os --build-hash-table true --ht-reference /path/GRCh38/hg38.fa --output-directory /path/GRCh38/dragmapindex/

and get: Segmentation fault (core dumped)

Is there something wrong I did?

I tried to use dragen-os on a pair of gzipped fastq files and it gave me this feed back:

''' dragen-os: /software/dragmap/1.1.2/src/lib/workflow/DualFastq2SamWorkflow.cpp:64: dragenos::align::InsertSizeParameters dragenos::workflow::DualFastq2SamWorkflow::requestInsertSizeInfo(dragenos::align::InsertSizeDistribution&, std::istream&, std::istream&): Assertion `inputR1.eof()' failed. ''' It seems the gzip fq file does not have a valid EOF But I checked the gzip file with gzip -v -t and it returned True.

Then I gunzip the fq files and input to dragen-os and it gave me the same error. While both versions of the pair of fq files can be used to run bwa-mem without errors.

Last, I tried to use another pair of gzipped fq files from another sequencing provider (platform Illumina) and dragen-os finished with no errors.

Therefore, I wonder:

1. Is this a bug?
2. If not a but, is dragen-os applied to Illumina system generated fq files only?
3. If 2, and if I want to use dragmap to process some simulation fastq files, what kind of format should I follow to make the simulated fastq files pass the dragmap format check?

Much appreciated!

I hit a segmentation fault on this read pair from HG002. Index is built with hg38 reference.

dragmap_1.fastq.txt dragmap_2.fastq.txt

Failing line

Program received signal SIGSEGV, Segmentation fault.
0x00000000004ace0a in banded_sw (unclippedReadLen=251, read_begin=0, n=<optimized out>, mat=<optimized out>, band_width=1, weight_gapE=1, weight_gapO=7, score=<optimized out>, readLen=1, refLen=1,
    read=<optimized out>, ref=0xffffffffffffffff <Address 0xffffffffffffffff out of bounds>) at ./dragmap/thirdparty/sswlib/ssw/ssw.c:784
784                                     temp2 = h_b[d] + mat[ref[j] * n + read[i]] + bonus;

gdb stack trace

#0  0x00000000004ace0a in banded_sw (unclippedReadLen=251, read_begin=0, n=<optimized out>, mat=<optimized out>, band_width=1, weight_gapE=1, weight_gapO=7, score=<optimized out>, readLen=1, refLen=1,
    read=<optimized out>, ref=0xffffffffffffffff <Address 0xffffffffffffffff out of bounds>) at ./dragmap/thirdparty/sswlib/ssw/ssw.c:784
#1  ssw_align (prof=<optimized out>, ref=<optimized out>, refLen=1, weight_gapO=<optimized out>, weight_gapE=<optimized out>, flag=<optimized out>, filters=0, filterd=0, maskLen=125)
    at ./dragmap/thirdparty/sswlib/ssw/ssw.c:1029
#2  0x0000000000445f5f in dragenos::align::VectorSmithWaterman::align (this=0x7fffffffac50, queryBegin=<optimized out>, queryEnd=<optimized out>, databaseBegin=0x0, databaseEnd=0x0,
    reverseQuery=<optimized out>, cigar=...) at ./dragmap/src/lib/align/VectorSmithWaterman.cpp:67
#3  0x0000000000436848 in dragenos::align::AlignmentGenerator::generateAlignment ([email protected]=0x7fffffffacb8, alnMinScore=22, read=..., seedChain=..., alignment=...)
    at ./dragmap/src/lib/align/AlignmentGenerator.cpp:145
#4  0x0000000000430786 in dragenos::align::Aligner::getAlignments ([email protected]=0x7fffffffa750, readPair=..., alignmentPairs=..., insertSizeParameters=..., pairBuilder=...)
    at ./dragmap/src/lib/align/Aligner.cpp:718
#5  0x0000000000427e1f in alignAndStorePair<dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq(std::istream&, std::istream&, std::ostream&, std::ostream&, std::ostream&)::__lambda10::__lambda12> (
    store=..., alignmentPairs=..., pairBuilder=..., singlePicker=..., aligner=..., pair=..., insertSizeParameters=...)
    at ./dragmap/src/include/workflow/alignment/AlignmentUtils.hpp:199
#6  alignDualFastq<dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq(std::istream&, std::istream&, std::ostream&, std::ostream&, std::ostream&)::__lambda10::__lambda12> (this=0x7fffffffc280,
    store=..., pairBuilder=..., singlePicker=..., aligner=..., inputR2=..., inputR1=..., insertSizeParameters=...) at ./dragmap/src/lib/workflow/DualFastq2SamWorkflow.cpp:107
#7  dragenos::workflow::DualFastq2SamWorkflow::__lambda10::operator() (__closure=0x7fffffffb220, lock=...) at ./dragmap/src/lib/workflow/DualFastq2SamWorkflow.cpp:396
#8  0x00000000004292be in execute (lock=..., this=0x7fffffffb050) at ./dragmap/src/include/common/Threads.hpp:188
#9  unsafeExecute (executor=0x7fffffffb050, lock=..., this=0x8ff500 <dragenos::common::CPU_THREADS(unsigned long)::pool>) at ./dragmap/src/include/common/Threads.hpp:314
#10 safeExecute (executor=0x7fffffffb050, lock=..., this=0x8ff500 <dragenos::common::CPU_THREADS(unsigned long)::pool>) at ./dragmap/src/include/common/Threads.hpp:332
#11 execute<dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq(std::istream&, std::istream&, std::ostream&, std::ostream&, std::ostream&)::__lambda10> (threads=56, func=..., lock=...,
    this=0x8ff500 <dragenos::common::CPU_THREADS(unsigned long)::pool>) at ./dragmap/src/include/common/Threads.hpp:201
#12 execute<dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq(std::istream&, std::istream&, std::ostream&, std::ostream&, std::ostream&)::__lambda10> (threads=56, func=...,
    this=0x8ff500 <dragenos::common::CPU_THREADS(unsigned long)::pool>) at ./dragmap/src/include/common/Threads.hpp:167
#13 dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq ([email protected]=0x7fffffffc280, r1Stream=..., r2Stream=..., os=..., insertSizeDistributionLogStream=..., mappingMetricsLogStream=...)
    at ./dragmap/src/lib/workflow/DualFastq2SamWorkflow.cpp:446
#14 0x000000000042a579 in dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq ([email protected]=0x7fffffffc280, os=..., insertSizeDistributionLogStream=..., mappingMetricsLogStream=...)
    at ./dragmap/src/lib/workflow/DualFastq2SamWorkflow.cpp:188
#15 0x000000000040ae85 in dragenos::workflow::input2Sam (options=...) at ./dragmap/src/lib/workflow/Input2SamWorkflow.cpp:569
#16 0x0000000000408ac8 in dragenos::common::run<dragenos::options::DragenOsOptions> (callback=0x40a740 <dragenos::workflow::input2Sam(dragenos::options::DragenOsOptions const&)>, [email protected]=11,
    [email protected]=0x7fffffffd308) at ./dragmap/src/include/common/Program.hpp:93
#17 0x0000000000402499 in main (argc=11, argv=0x7fffffffd308) at ./dragmap/src/dragen-os.cpp:24

Command line:

./build/release/dragen-os -r ./index -1 dragmap_1.fastq -2 dragmap_1.fastq  --output-directory ./sam --output-file-prefix dragmap

System configuration: Centos 7.6, gcc 4.8.5, boost 1.53.0, zlib 1.2.11

Thanks for looking into this. Let me know if you require any more details.

Hello there,

Thank you for maintaining this awesome open-source version of Dragen's aligner! I was planning on replacing bwa-mem2 with dragmap for its slightly higher accuracy. We have internally benchmarked it, and it seems to perform better.

I just have a quick question. Do you have a Dockerfile for building an image of this tool? I peeked around Dockerhub and saw a few images exist for DRAGMAP, but they didn't look too promising after taking a closer look. I was planning on building an image for our pipeline if one does not exist. If you want, I can send you the final Dockerfile.

Please let me know what you think.

Best Regards, @skchronicles

I thought the benefit of the dragmap aligner was supposed to be its superior handling of ALT contigs in GRCh38 (compared to bwa mem). But the --ht-alt-liftover option does not look to be supported. I find "config->altLiftover" in the source code but no way to configure/enable it from the command line. Can anyone clarify if GRCh38 ALT-awareness is supported in the current release? And if yes, how to use it. And if no, if it is planned and for when? Thx.

When I follow the instructions in the README I get the following error:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - dragmap

Current channels:

  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

I think the correct command is conda install -c bioconda dragmap. But when I try that, I get another error.

jmschr:/users/jmschr/github$ conda install -c bioconda dragmap
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: | 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                 

UnsatisfiableError: 

I'm on Ubuntu 18.04.6 LTS and used a fresh conda environment running Python 3.8.3 with GCC 7.3.0.

Hi there,

I'm getting the following error on some in house generated data:

2022-01-24 17:24:34     [7f49749857c0]  Version: 66742900
2022-01-24 17:24:34     [7f49749857c0]  argc: 9 argv: dragen-os --num-threads 16 -r /analysis/dragmap_test/gca -1 sample-dna-1-1_S7_R1_001.fastq.gz -2 sample-dna-1-1_S7_R2_001.fastq.gz
decompHashTableCtxInit...
  0.932 seconds
decompHashTableHeader...
  0.001 seconds
decompHashTableLiterals...
  3.131 seconds
decompHashTableExtIndex...
  0.058 seconds
decompHashTableAutoHits...
  20.644 seconds
decompHashTableSetFlags...
  1.207 seconds
finished decompress
Running dual fastq workflow on 16 threads. System supports 96 threads.
0       249     0       0       0       0       10000   1       40000   1       1000    0       0       0       6
0       250     0       0       0       0       10000   1       40000   1       1000    0       0       0       5
0       251     0       0       0       0       10000   1       40000   1       1000    0       0       0       4
0       252     0       0       0       0       10000   1       40000   1       1000    0       0       0       3
0       253     0       0       0       0       10000   1       40000   1       1000    0       0       0       2
0       254     0       0       0       0       10000   1       40000   1       1000    0       0       0       1
0       0       165     212     274     224.484 79.2253 1       601     26      423     91232   91986   0       0
Initial paired-end statistics detected for read group all, based on 91232 high quality pairs for FR orientation
        Quartiles (25 50 75) = 165 212 274
        Mean = 224.484
        Standard deviation = 79.2253
        Rescue radius = 198.063
        Effective rescue sigmas = 2.5
        Boundaries for mean and standard deviation: low = 1, high = 492
        Boundaries for proper pairs: low = 1, high = 601
        NOTE: DRAGEN's insert estimates include corrections for clipping (so they are not identical to TLEN)
[139951751513856]       ERROR: This thread caught an exception first
Error: : Invalid argument: /tools/DRAGMAP-1.2.1/src/lib/sequences/Seed.cpp(64): Throw in function dragenos::sequences::Seed::Data dragenos::sequences::Seed::getPrimaryData(bool) const
Dynamic exception type: boost::exception_detail::clone_impl<dragenos::common::PreConditionException>
std::exception::what: Requesting primary data for an invalid seed
: Requesting primary data for an invalid seed

I am using GCA_000001405.15 as my reference. I could use the same reference to map some reads from the 1000 Genomes Project but I'm only getting the above error with the in house generated data (which can be mapped using BWA MEM).

Unfortunately, I can't share the data but may you let me know how I can troubleshoot the issue? (I get the same error with the latest (commit) version of DRAGMAP.

Thank you, Dave

Hi, I'm trying to create docker container of the newest version of Dragmap, but am getting the following error:

#0 291.9 making /DRAGMAP-1.3.0/build/release/common/SystemCompatibility.o
#0 294.6 /DRAGMAP-1.3.0/src/lib/common/SystemCompatibility.cpp: In function 'void dragenos::common::configureMemoryManagement(bool, bool)':
#0 294.6 /DRAGMAP-1.3.0/src/lib/common/SystemCompatibility.cpp:382:13: error: 'M_ARENA_MAX' was not declared in this scope
#0 294.6   382 |     mallopt(M_ARENA_MAX, 1);
#0 294.6       |             ^~~~~~~~~~~
#0 294.6 /DRAGMAP-1.3.0/src/lib/common/SystemCompatibility.cpp:382:5: error: 'mallopt' was not declared in this scope; did you mean 'malloc'?
#0 294.6   382 |     mallopt(M_ARENA_MAX, 1);
#0 294.6       |     ^~~~~~~
#0 294.6       |     malloc
#0 294.6 /DRAGMAP-1.3.0/src/lib/common/SystemCompatibility.cpp:392:13: error: 'M_MXFAST' was not declared in this scope
#0 294.6   392 |     mallopt(M_MXFAST, 0);
#0 294.6       |             ^~~~~~~~
#0 294.6 /DRAGMAP-1.3.0/src/lib/common/SystemCompatibility.cpp:392:5: error: 'mallopt' was not declared in this scope; did you mean 'malloc'?
#0 294.6   392 |     mallopt(M_MXFAST, 0);
#0 294.6       |     ^~~~~~~
#0 294.6       |     malloc
#0 295.1 make: *** [/DRAGMAP-1.3.0/make/lib.mk:110: /DRAGMAP-1.3.0/build/release/common/SystemCompatibility.o] Error 1

This is my code used to create the docker image:

FROM alpine:3.16.0

RUN apk update && \
    apk add bash boost-dev g++ gtest-dev make zlib-dev && \
    wget -qO- "https://github.com/Illumina/DRAGMAP/archive/refs/tags/1.3.0.tar.gz" | tar -zx && \
    cd DRAGMAP-* && \
    make && \
    make install && \
    cd .. && \
    rm -rf DRAGMAP-*

Does anyone know what I can do to fix this? Thanks in advance :)

Hello. I'm using DRAGMAP for mapping. I have the results of Dragen's same mapping.

When I use Dragen-os :

dragen-os --build-hash-table true --ht-reference {input.fa} --output-directory {output}

dragen-os -r {params.refdir} -1 {input.input1} -2 {input.input2} --ht-decoys {input.decoy} --output-directory {params.outdir} --output-file-prefix {wildcards.sample}_{wildcards.run}

And I have a problem with one of the result in the summary :

MAPPING/ALIGNING SUMMARY,,Number of duplicate marked and mate reads removed,0,0.00 MAPPING/ALIGNING SUMMARY,,Number of unique reads (excl. duplicate marked reads),60409748,100.00

And if I run the same mapping with dragen in baseSpace :

Number of duplicate marked reads 30,021,566 Number of duplicate marked reads (%) 49.7 Number of unique reads (excl. duplicate marked reads) 30,388,182 Number of unique reads (excl. duplicate marked reads) (%) 50.3

What's happens here? Is there any option in dragen-os to see duplicated reads ?

Thank you very much

I was trying out DRAGMAP to align one of the Illumina Platinum Genome datasets: fastq1, fastq2 and hit a segmentation fault after aligning around ~86 million reads to the hg38 reference genome.

gdb reports this line:

generateSequence<dragenos::sequences::Read, dragenos::align::Alignment> (a=..., read=..., os=...) at ./dragmap/src/include/align/Sam.hpp:127
127             os << ReadT::decodeRcBase(*it);

Here is the backtrace:

#0  generateSequence<dragenos::sequences::Read, dragenos::align::Alignment> (a=..., read=..., os=...) at ./dragmap/src/include/align/Sam.hpp:127
#1  dragenos::align::Sam::generateRecord<dragenos::sequences::Read, dragenos::align::Alignment> (this=0x7fffffffb100, os=..., read=..., alignment=..., rgid="1")
    at ./dragmap/src/include/align/Sam.hpp:73
#2  0x000000000043b55c in dragenos::workflow::DualFastq2SamWorkflow::__lambda10::__lambda12::operator() ([email protected]=0x7fff8378cf80, r=..., a=...)
    at ./dragmap/src/lib/workflow/DualFastq2SamWorkflow.cpp:379
#3  0x000000000043bda9 in dragenos::workflow::alignment::storePeSupplementary<dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq(std::istream&, std::istream&, std::ostream&, std::ostream&, std::ostream&)::__lambda10::__lambda12>(const dragenos::align::SinglePicker &, const dragenos::sequences::Read &, dragenos::align::Aligner::Alignments &, dragenos::align::Alignment *, const dragenos::align::Alignment &, dragenos::workflow::DualFastq2SamWorkflow::__lambda10::__lambda12, const dragenos::align::InsertSizeParameters &) (singlePicker=..., read=..., alignments=..., primary=0x7ff1f49285e0, mate=...,
    store=..., insertSizeParameters=...) at ./dragmap/src/include/workflow/alignment/AlignmentUtils.hpp:90
#4  0x000000000043e1ae in alignAndStorePair<dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq(std::istream&, std::istream&, std::ostream&, std::ostream&, std::ostream&)::__lambda10::__lambda12> (
    store=..., alignmentPairs=std::vector of length 32, capacity 512 = {...}, pairBuilder=..., singlePicker=..., aligner=..., pair=..., insertSizeParameters=...)
    at ./dragmap/src/include/workflow/alignment/AlignmentUtils.hpp:233
#5  alignDualFastq<dragenos::workflow::DualFastq2SamWorkflow::parseDualFastq(std::istream&, std::istream&, std::ostream&, std::ostream&, std::ostream&)::__lambda10::__lambda12> (this=0x7fffffffc400,
    store=..., pairBuilder=..., singlePicker=..., aligner=..., inputR2=..., inputR1=..., insertSizeParameters=...) at ./dragmap/src/lib/workflow/DualFastq2SamWorkflow.cpp:107
#6  dragenos::workflow::DualFastq2SamWorkflow::__lambda10::operator() (__closure=0x7fffffffb3a0, lock=...) at ./dragmap/src/lib/workflow/DualFastq2SamWorkflow.cpp:396
#7  0x000000000048e5e6 in unsafeExecute (executor=0x7fffffffb1d0, lock=..., this=0x724620 <dragenos::common::CPU_THREADS(unsigned long)::pool>)
    at ./dragmap/src/include/common/Threads.hpp:314
#8  safeExecute (executor=0x7fffffffb1d0, lock=..., this=0x724620 <dragenos::common::CPU_THREADS(unsigned long)::pool>) at /x/arunsub/winter_21/dragmap/src/include/common/Threads.hpp:332
#9  executeAllPending (lock=..., this=0x724620 <dragenos::common::CPU_THREADS(unsigned long)::pool>) at ./dragmap/src/include/common/Threads.hpp:371
#10 dragenos::common::BasicThreadPool<false>::threadFunc (this=0x724620 <dragenos::common::CPU_THREADS(unsigned long)::pool>) at ./dragmap/src/include/common/Threads.hpp:350
#11 0x00007ffff6799070 in ?? () from /usr/lib64/libstdc++.so.6
#12 0x00007ffff60a1ea5 in start_thread () from /usr/lib64/libpthread.so.0
#13 0x00007ffff58b28dd in clone () from /usr/lib64/libc.so.6

Command line:

./build/release/dragen-os -r ./index -1 ERR194147_1.fastq.gz -2 ERR194147_2.fastq.gz --output-directory ./sam --output-file-prefix ERR194147

System configuration: Centos 7.6, gcc 4.8.5, boost 1.53.0, zlib 1.2.11

Thanks for looking into this.

Compilation fails at this step:

g++ -MT /src/DRAGMAP-1.2.1/build/release/common/SystemCompatibility.o -MMD -MP -MF /src/DRAGMAP-1.2.1/build/release/common/SystemCompatibility.Td -Wall -ggdb3 -DLOCAL_BUILD -D'DRAGEN_OS_VERSION="0.2020.08.19"'  -DVERSION_STRING="UNKNOWN" -I /src/DRAGMAP-1.2.1/thirdparty -I /src/DRAGMAP-1.2.1/src/include -I /src/DRAGMAP-1.2.1/thirdparty/dragen/src -I /src/DRAGMAP-1.2.1/thirdparty/dragen/src/common/public  -I /src/DRAGMAP-1.2.1/thirdparty/dragen/src/host/metrics/public -I /src/DRAGMAP-1.2.1/thirdparty/sswlib -I /src/DRAGMAP-1.2.1/stubs/dragen/src/host/dragen_api -I /src/DRAGMAP-1.2.1/stubs/dragen/src/host/dragen_api/dbam  -I /src/DRAGMAP-1.2.1/stubs/dragen/src/host/infra/public -I /src/DRAGMAP-1.2.1/stubs/dragen/src/host/metrics/public -Wfatal-errors -g -msse4.2 -O2 -ftree-vectorize -finline-functions -fpredictive-commoning -fgcse-after-reload -funswitch-loops -ftree-slp-vectorize -fvect-cost-model -fipa-cp-clone -ftree-phiprop -std=c++11 -c -o /src/DRAGMAP-1.2.1/build/release/common/SystemCompatibility.o /src/DRAGMAP-1.2.1/src/lib/common/SystemCompatibility.cpp
/src/DRAGMAP-1.2.1/src/lib/common/SystemCompatibility.cpp: In function 'void dragenos::common::configureMemoryManagement(bool, bool)':
/src/DRAGMAP-1.2.1/src/lib/common/SystemCompatibility.cpp:401:13: error: 'M_ARENA_MAX' was not declared in this scope
  401 |     mallopt(M_ARENA_MAX, 1);
      |             ^~~~~~~~~~~
compilation terminated due to -Wfatal-errors.
make: *** [/src/DRAGMAP-1.2.1/make/lib.mk:113: /src/DRAGMAP-1.2.1/build/release/common/SystemCompatibility.o] Error 1

The -V command line option does not seem to work as expected:

$ dragen-os -V
UNKNOWN

Also, the @PG line in the BAM files generated by the dragen-os command has an incorrect empty space next to the "ID:" field name, plus it doesn't state DRAGMAP, but DRAGEN-OS instead:

@PG     ID: DRAGEN-OS   VN:0.2020.08.19 CL:dragen-os ...

Finally, if version 0.2020.08.19 stored in BAM files means August 19th 2020, maybe the version numbering should be updated too.

Hello, Thank you for making DRAGMAP available to install.

1. I tried to install it using conda install -c bioconda dragmap but I could not get the latest version as follow: Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for: dragmap -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0'] dragmap -> zlib[version='>=1.2.12,<1.3.0a0'] -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0'] python=3.7 -> libgcc-ng[version='>=11.2.0|>=7.5.0|>=7.3.0|>=7.2.0']

Package libstdcxx-ng conflicts for: python=3.7 -> libffi[version='>=3.4,<3.5'] -> libstdcxx-ng[version='>=11.2.0|>=7.5.0'] python=3.7 -> libstdcxx-ng[version='>=7.2.0|>=7.3.0']The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.31=0
• feature:|@/linux-64::__glibc==2.31=0
• dragmap -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

However, when I run dragen-os --help, I got the message "command not found".

• ===============================================================================

2. I also tried to install it using the following code: wget --no-check-certificate https://github.com/Illumina/DRAGMAP/archive/refs/tags/${VERSION}.tar.gz \

&& tar -xvf ${VERSION}.tar.gz \
&& rm ${VERSION}.tar.gz \
&& cd DRAGMAP-${VERSION} \
&& make \
&& make install \
&& dragen-os --help

But I got the following error:

--2022-12-15 21:59:07-- https://github.com/Illumina/DRAGMAP/archive/refs/tags/.tar.gz Resolving github.com (github.com)... 140.82.121.3 Connecting to github.com (github.com)|140.82.121.3|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://codeload.github.com/Illumina/DRAGMAP/tar.gz/refs/tags/ [following] --2022-12-15 21:59:07-- https://codeload.github.com/Illumina/DRAGMAP/tar.gz/refs/tags/ Resolving codeload.github.com (codeload.github.com)... 140.82.121.10 Connecting to codeload.github.com (codeload.github.com)|140.82.121.10|:443... connected. HTTP request sent, awaiting response... 400 Bad Request 2022-12-15 21:59:08 ERROR 400: Bad Request. ` Kindly, would you please be able to guide me to install DRAGMAP latest version?

Many thanks for your help!

Maged

build environment

Ubuntu 18.04.6 LTS gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04) Intel(R) oneAPI DPC++/C++ Compiler 2022.2.0 (2022.2.0.20220730) boost 1.58

run environment

hardware

2x Intel Xeon Gold 6342 2TB RAM (16x 128GB DDR4-3200) 4x 4TB PCI-E 4.0 NVME SSD RAID 0 (ref and input here)

system

Ubuntu 22.04.1 LTS

common options

--ref-load-hash-bin 1 --mmap-reference 1

data

board institute gatk bundle hg38 + using alt-masked bed file inhouse wes 200x coverage 150bp paied-end

MAPPING/ALIGNING SUMMARY,,Total input reads,142688722,100.00
MAPPING/ALIGNING SUMMARY,,Number of duplicate marked reads,0,0.00
MAPPING/ALIGNING SUMMARY,,Number of duplicate marked and mate reads removed,0,0.00
MAPPING/ALIGNING SUMMARY,,Number of unique reads (excl. duplicate marked reads),142688722,100.00
MAPPING/ALIGNING SUMMARY,,Reads with mate sequenced,142688722,100.00
MAPPING/ALIGNING SUMMARY,,Reads without mate sequenced,0,0.00
MAPPING/ALIGNING SUMMARY,,QC-failed reads,0,0.00
MAPPING/ALIGNING SUMMARY,,Mapped reads,142533774,99.89
MAPPING/ALIGNING SUMMARY,,Mapped reads adjusted for filtered mapping,142533774,99.89
MAPPING/ALIGNING SUMMARY,,Mapped reads R1,71304146,99.94
MAPPING/ALIGNING SUMMARY,,Mapped reads R2,71229628,99.84
MAPPING/ALIGNING SUMMARY,,Number of unique & mapped reads (excl. duplicate marked reads),142533774,99.89
MAPPING/ALIGNING SUMMARY,,Unmapped reads,154948,0.11
MAPPING/ALIGNING SUMMARY,,Unmapped reads adjusted for filtered mapping,154948,0.11
MAPPING/ALIGNING SUMMARY,,Adjustment of reads matching non-reference decoys,0,0.00
MAPPING/ALIGNING SUMMARY,,Singleton reads (itself mapped; mate unmapped),110302,0.08
MAPPING/ALIGNING SUMMARY,,Paired reads (itself & mate mapped),142423472,99.81
MAPPING/ALIGNING SUMMARY,,Properly paired reads,141084044,98.88
MAPPING/ALIGNING SUMMARY,,Not properly paired reads (discordant),1339428,0.94
MAPPING/ALIGNING SUMMARY,,Paired reads mapped to different chromosomes,142423472,100.00
MAPPING/ALIGNING SUMMARY,,Paired reads mapped to different chromosomes (MAPQ>=10),133005934,93.39
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [40:inf),124162867,87.02
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [30:40),2394718,1.68
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [20:30),3708424,2.60
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [10:20),2812611,1.97
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ [ 0:10),9455154,6.63
MAPPING/ALIGNING SUMMARY,,Reads with MAPQ NA (Unmapped reads),154948,0.11
MAPPING/ALIGNING SUMMARY,,Reads with indel R1,857524,1.20
MAPPING/ALIGNING SUMMARY,,Reads with indel R2,871870,1.22
MAPPING/ALIGNING SUMMARY,,Total bases,21545997022
MAPPING/ALIGNING SUMMARY,,Total bases R1,10772998511
MAPPING/ALIGNING SUMMARY,,Total bases R2,10772998511
MAPPING/ALIGNING SUMMARY,,Mapped bases R1,10766926046
MAPPING/ALIGNING SUMMARY,,Mapped bases R2,10755673828
MAPPING/ALIGNING SUMMARY,,Soft-clipped bases R1,773694088,7.19
MAPPING/ALIGNING SUMMARY,,Soft-clipped bases R2,802316036,7.46
MAPPING/ALIGNING SUMMARY,,Mismatched bases R1,26865434,0.25
MAPPING/ALIGNING SUMMARY,,Mismatched bases R2,35386201,0.33
MAPPING/ALIGNING SUMMARY,,Mismatched bases R1 (excl. indels),24746504,0.23
MAPPING/ALIGNING SUMMARY,,Mismatched bases R2 (excl. indels),33232164,0.31
MAPPING/ALIGNING SUMMARY,,Q30 bases,19997458379,92.81
MAPPING/ALIGNING SUMMARY,,Q30 bases R1,10094153115,93.70
MAPPING/ALIGNING SUMMARY,,Q30 bases R2,9903305264,91.93
MAPPING/ALIGNING SUMMARY,,Total alignments,144115736
MAPPING/ALIGNING SUMMARY,,Secondary alignments,0
MAPPING/ALIGNING SUMMARY,,Supplementary (chimeric) alignments,1581962
MAPPING/ALIGNING SUMMARY,,Estimated read length,151.00

original 1.3.0

MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [thousand reads/second],330.71
        User time (seconds): 32616.91
        System time (seconds): 132.32
        Percent of CPU this job got: 7580%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 7:12.02
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 55974088
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 364
        Minor (reclaiming a frame) page faults: 58609499
        Voluntary context switches: 792066
        Involuntary context switches: 87493
        Swaps: 0
        File system inputs: 72
        File system outputs: 32
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

changed gcc opt options (sse2 only)

CPPFLAGS += -march=x86-64 -O3 -ftree-vectorize -fvect-cost-model=cheap 

MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [thousand reads/second],305.52
        User time (seconds): 37615.52
        System time (seconds): 126.13
        Percent of CPU this job got: 8078%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 7:47.21
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 55965548
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 272
        Minor (reclaiming a frame) page faults: 57129594
        Voluntary context switches: 752958
        Involuntary context switches: 129579
        Swaps: 0
        File system inputs: 1064
        File system outputs: 32
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

icc skylake-avx512

CPPFLAGS += -xSKYLAKE-AVX512 -O3 

MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [thousand reads/second],356.07
        User time (seconds): 20044.17
        System time (seconds): 99.55
        Percent of CPU this job got: 5020%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 6:41.21
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 55977116
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 462
        Minor (reclaiming a frame) page faults: 61073017
        Voluntary context switches: 1047728
        Involuntary context switches: 41240
        Swaps: 0
        File system inputs: 0
        File system outputs: 32
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

icc icelake-server

CPPFLAGS += -xICELAKE-SERVER -O3 

MAPPING/ALIGNING SUMMARY,,DRAGEN mapping rate [thousand reads/second],353.45
        User time (seconds): 20134.72
        System time (seconds): 102.66
        Percent of CPU this job got: 5009%
        Elapsed (wall clock) time (h:mm:ss or m:ss): 6:43.96
        Average shared text size (kbytes): 0
        Average unshared data size (kbytes): 0
        Average stack size (kbytes): 0
        Average total size (kbytes): 0
        Maximum resident set size (kbytes): 55977712
        Average resident set size (kbytes): 0
        Major (requiring I/O) page faults: 202
        Minor (reclaiming a frame) page faults: 60891037
        Voluntary context switches: 1044493
        Involuntary context switches: 40804
        Swaps: 0
        File system inputs: 0
        File system outputs: 32
        Socket messages sent: 0
        Socket messages received: 0
        Signals delivered: 0
        Page size (bytes): 4096
        Exit status: 0

Hi,

I am running dragmap 1.3.0 on some small test data and continue to get a failure with

0 Segmentation fault      dragen-os -r dragmap --num-threads 2 -1 test_1.fastq.gz -2 test_2.fastq.gz 2> test.sorted.dragmap.log
          31 Done                    | samtools sort --threads 2 -o test.sorted.bam -

as soon as I downgrade back to 1.2.1, it works on the same data/setup.

Command run:

  dragen-os \
      -r dragmap \
       \
      --num-threads 2 \
      -1 test_1.fastq.gz -2 test_2.fastq.gz \
      2> test.sorted.dragmap.log \
      | samtools sort  --threads 2 -o test.sorted.bam -

The SAM header @RG sub field "PL" is listed as PL0 at https://github.com/Illumina/DRAGMAP/blob/2e0ec6856bf88f869e89283b650ada53bac75d80/src/include/sam/SamGenerator.hpp#L173

This is being reported by users as turning up in data, which will cause problems for any data which validates the input matches the specifications. The default from DRAGMAP should be ILLUMINA. This field is a controlled vocabulary, designed to allow users to tune their algorithms to the type of data being generated. The PM field (Platform Model) is more flexible and permits additional machine details.

Reported via https://github.com/samtools/hts-specs/issues/679

I have installed Dragmap successfully in two different servers. In one serve, when I ran it I got an error: Illegal instruction (core dumped). Can anyone help me please? CPU model: Intel(R) Xeon(R) CPU E7-8870 v2 @ 2.30GHz It works perfectly in the other server.