spades
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ablab
spades-3.11.0 :: config.info included *.info files not found.
Hello
while running SPAdes-3.11.0 one of our users reported the following problem.
spades.py --meta -1 file1.fastq -2 file.fastq -o test/ -t 4
ends with the following error
== Running assembler: K21
Exception caught /scratch/eric/test/K21/configs/config.info(3): cannot open include file simplification.info
== Error == system call for: "['/mount/gensoft2/exe/SPAdes/3.11.0/bin/spades', '/scratch/eric/test/K21/configs/config.info', '/scratch/eric/test/K21/configs/mda_mode.info', '/scratch/eric/test/K21/configs/meta_mode.info']" finished abnormally, err code: 4
when checking the file config.info from test/configs/debruijn/config.info one ca notice the following. incudes are relative.
; input options:
#include "simplification.info"
#include "construction.info"
#include "distance_estimation.info"
#include "detail_info_printer.info"
#include "tsa.info"
#include "pe_params.info"
K 55
after some code reading I ended hacking spades_logic.py (plain old patch attached) to generate a config.info file that handles the full path for the included files regarding the running configuration directory.
eg it will have something like that.
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/simplification.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/construction.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/distance_estimation.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/detail_info_printer.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/tsa.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/pe_params.info"
instead of just plain file name.
with this patch applied, spades hapilly runs to the normal end and provides expected results
let me know what you think about this patch.
NB as far as I understand the code config files are copied from share/spades/config files. maybee installer can set those path at install time.
regards
Eric
here are the relelvant part of the makefile used in our install framework
SRC= /local/gensoft2/src/SPAdes/SPAdes-3.11.0
EXE= /local/gensoft2/exe/SPAdes/3.11.0
BUILD= $(SRC)/build
build:
cd $(BUILD)
test -d $(BUILD) || $(MKDIR) -p $(BUILD)
cd $(BUILD) && module load gcc/4.9.4 cmake/3.2.1 && cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$(EXE) $(SRC)/src
cd $(BUILD) && module load gcc/4.9.4 && make -j `nproc`
install:
cd $(BUILD) && make install
Could you please post the build log as well? All the files are in the project configs directory and therefore no explicit path adjustment is necessary at all.
Hello
I installed SPADES-3.13.0 from source today and try to run some --test commands. and truspades failed with following error message
bigmess:SPAdes/3.13.0 > truspades.py --test
Generating truseq dataset from input directories:
/mount/gensoft2/exe/SPAdes/3.13.0/share/spades/test_dataset_truspades
Printing dataset to /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/dataset.info
Dataset generated. See result in /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/dataset.info
Launching truSPAdes assembly in 8 threads
You can find logs for separate barcodes in /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/logs
Starting: BC_A
Starting: BC_B
Failed to finish: BC_B
Failed to finish: BC_A
2 barcodes failed to assemble
Warning: could not find assembly results for barcode BC_A
Warning: could not find assembly results for barcode BC_B
Assembled virtual long TruSeq reads can be found in /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/TSLR.fasta
TruSPAdes launch successfully finished
TruSPAdes test launch failed: incorrect output files
while lookig at logs
bigmess:SPAdes/3.13.0 > tail /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/logs/BC_A.log
== Running assembler: K21
Exception caught /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_A/K21/configs/config.info(3): cannot open include file simplification.info
== Error == system call for: "['/mount/gensoft2/exe/SPAdes/3.13.0/bin/spades-core', '/mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_A/K21/configs/config.info', '/mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_A/K21/configs/moleculo_mode.info']" finished abnormally, err code: 4
In case you have troubles running SPAdes, you can write to [email protected]
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
same on other log file
bigmess:SPAdes/3.13.0 > tail /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/logs/BC_B.log
== Running assembler: K21
Exception caught /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_B/K21/configs/config.info(3): cannot open include file simplification.info
== Error == system call for: "['/mount/gensoft2/exe/SPAdes/3.13.0/bin/spades-core', '/mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_B/K21/configs/config.info', '/mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_B/K21/configs/moleculo_mode.info']" finished abnormally, err code: 4
In case you have troubles running SPAdes, you can write to [email protected]
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
Logs:
-- The C compiler identification is GNU 6.3.0 -- The CXX compiler identification is GNU 6.3.0 -- Check for working C compiler: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-6.3.0-4h22ps2wttqbknmpnjft4h5bd2uvzndl/bin/cc -- Check for working C compiler: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-6.3.0-4h22ps2wttqbknmpnjft4h5bd2uvzndl/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-6.3.0-4h22ps2wttqbknmpnjft4h5bd2uvzndl/bin/c++ -- Check for working CXX compiler: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-6.3.0-4h22ps2wttqbknmpnjft4h5bd2uvzndl/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done Setting default build configuration: RelWithAsserts CMake Warning (dev) at /pbtech_mounts/softlib001/apps/EL6/spack/opt/spack/linux-rhel6-x86_64/gcc-6.3.0/cmake-3.9.4-v3w54bykdxdf23psa6qe3yxyiwhchbob/share/cmake-3.9/Modules/FindOpenMP.cmake:200 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning.
Quoted variables like "c" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /pbtech_mounts/softlib001/apps/EL6/spack/opt/spack/linux-rhel6-x86_64/gcc-6.3.0/cmake-3.9.4-v3w54bykdxdf23psa6qe3yxyiwhchbob/share/cmake-3.9/Modules/FindOpenMP.cmake:324 (_OPENMP_GET_FLAGS) cmake/deps.cmake:16 (find_package) CMakeLists.txt:52 (include) This warning is for project developers. Use -Wno-dev to suppress it.
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found BZip2: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-6.3.0/bzip2-1.0.6-ikn3syj2vtwcbna4lykyinhp6ydvs7lv/lib/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Could NOT find readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY)
-- Boost version: 1.63.0
Making Release Configuration...
Building SPAdes from N/A, sha: N/A
-- Looking for include file features.h
-- Looking for include file features.h - found
-- Looking for include file sys/cdefs.h
-- Looking for include file sys/cdefs.h - found
-- Looking for atomic_fetchadd_long
-- Looking for atomic_fetchadd_long - not found
-- Looking for OSAtomicAdd64
-- Looking for OSAtomicAdd64 - not found
-- Looking for OSSpinLockLock
-- Looking for OSSpinLockLock - not found
-- Looking for malloc_thread_cleanup
-- Looking for malloc_thread_cleanup - not found
-- Looking for pthread_mutex_init_calloc_cb,
-- Looking for pthread_mutex_init_calloc_cb, - not found
-- Looking for sbrk
-- Looking for sbrk - found
-- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED
-- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED - Success
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of void*
-- Check size of void* - done
-- Performing Test JEMALLOC_TLS
-- Performing Test JEMALLOC_TLS - Success
-- Looking for memalign
-- Looking for memalign - found
-- Looking for valloc
-- Looking for valloc - found
-- Check size of int
-- Check size of int - done
-- Check size of long
-- Check size of long - done
-- Check size of intmax_t
-- Check size of intmax_t - done
-- Looking for open
-- Looking for open - found
-- Looking for include file execinfo.h
-- Looking for include file execinfo.h - found
-- Looking for include file signal.h
-- Looking for include file signal.h - found
-- Looking for include file sys/stat.h
-- Looking for include file sys/stat.h - found
-- Looking for include file cxxabi.h
-- Looking for include file cxxabi.h - not found
-- Looking for include file dlfcn.h
-- Looking for include file dlfcn.h - found
-- Looking for include file mach/mach.h
-- Looking for include file mach/mach.h - not found
-- Looking for include file link.h
-- Looking for include file link.h - found
-- Looking for backtrace
-- Looking for backtrace - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Looking for shm_open
-- Looking for shm_open - not found
-- Looking for shm_open in rt
-- Looking for shm_open in rt - found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dmm2017/cloudSPAdes-dev/build_spades
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/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c: In function ‘nlopt_minimize_constrained’:
/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c:149:6: warning: ‘nlopt_minimize_econstrained’ is deprecated [-Wdeprecated-declarations]
return nlopt_minimize_econstrained(
^~~~~~
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c:23:0:
/home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:350:28: note: declared here
NLOPT_EXTERN(nlopt_result) nlopt_minimize_econstrained(
^~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c: In function ‘nlopt_minimize’:
/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c:167:6: warning: ‘nlopt_minimize_constrained’ is deprecated [-Wdeprecated-declarations]
return nlopt_minimize_constrained(
^~~~~~
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c:23:0:
/home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:339:28: note: declared here
NLOPT_EXTERN(nlopt_result) nlopt_minimize_constrained(
^~~~~~~~~~~~~~~~~~~~~~~~~~
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/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/cdirect/hybrid.c: In function ‘optimize_rect’:
/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/cdirect/hybrid.c:91:6: warning: ‘nlopt_minimize’ is deprecated [-Wdeprecated-declarations]
ret = nlopt_minimize(p->local_alg, n, fcount, p,
^~~
In file included from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt-util.h:29:0,
from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/cdirect/hybrid.c:27:
/home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:329:28: note: declared here
NLOPT_EXTERN(nlopt_result) nlopt_minimize(
^~~~~~~~~~~~~~
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/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c: In function ‘trsapp’:
/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c:184:3: warning: ‘nlopt_minimize_constrained’ is deprecated [-Wdeprecated-declarations]
ret = nlopt_minimize_constrained(NLOPT_LD_MMA, *n, quad_model, &qmd,
^~~
In file included from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt-util.h:29:0,
from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/newuoa.h:4,
from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c:33:
/home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:339:28: note: declared here
NLOPT_EXTERN(nlopt_result) nlopt_minimize_constrained(
^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c: In function ‘biglag’:
/home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c:1241:3: warning: ‘nlopt_minimize_constrained’ is deprecated [-Wdeprecated-declarations]
return nlopt_minimize_constrained(NLOPT_LD_MMA, *n, lag, &ld,
^~~~~~
In file included from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt-util.h:29:0,
from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/newuoa.h:4,
from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c:33:
/home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:339:28: note: declared here
NLOPT_EXTERN(nlopt_result) nlopt_minimize_constrained(
^~~~~~~~~~~~~~~~~~~~~~~~~~
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[ 47%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o
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[ 49%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/block.c:5:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined
safe_mutex_unlock(pthread_mutex_t *mutex);
^~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined
safe_mutex_lock(pthread_mutex_t mutex);
^~~~~~~~~~~~~~~
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/block.c:4:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined
unpackInt16(const uint8_t buffer);
^~~~~~~~~~~
[ 49%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined
safe_mutex_unlock(pthread_mutex_t *mutex);
^~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined
safe_mutex_lock(pthread_mutex_t mutex);
^~~~~~~~~~~~~~~
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined
unpackInt16(const uint8_t buffer);
^~~~~~~~~~~
[ 49%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/kthread.c.o
[ 49%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined
safe_mutex_unlock(pthread_mutex_t *mutex);
^~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined
safe_mutex_lock(pthread_mutex_t mutex);
^~~~~~~~~~~~~~~
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined
unpackInt16(const uint8_t buffer);
^~~~~~~~~~~
[ 49%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/malloc_wrap.c.o
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In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined
safe_mutex_unlock(pthread_mutex_t *mutex);
^~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined
safe_mutex_lock(pthread_mutex_t *mutex);
^~~~~~~~~~~~~~~
[ 52%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined
safe_mutex_unlock(pthread_mutex_t *mutex);
^~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined
safe_mutex_lock(pthread_mutex_t mutex);
^~~~~~~~~~~~~~~
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined
unpackInt16(const uint8_t buffer);
^~~~~~~~~~~
[ 52%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o
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In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11:0,
from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined
safe_mutex_unlock(pthread_mutex_t *mutex);
^~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined
safe_mutex_lock(pthread_mutex_t mutex);
^~~~~~~~~~~~~~~
In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7:0:
/home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined
unpackInt16(const uint8_t buffer);
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/home/dmm2017/cloudSPAdes-dev/src/common/assembly_graph/graph_support/scaff_supplementary.cpp: In member function ‘bool path_extend::ScaffoldingUniqueEdgeAnalyzer::ConservativeByPaths(path_extend::EdgeId, const path_extend::GraphCoverageMap&, const path_extend::pe_config::LongReads&, int) const’:
/home/dmm2017/cloudSPAdes-dev/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:130:63: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
if (maxx < lr_config.unique_edge_priority * double(alt)) {
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[ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o
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[ 68%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o
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[ 69%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o
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[ 71%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o
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/home/dmm2017/cloudSPAdes-dev/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function ‘void coverage_model::KMerCoverageModel::Fit()’:
/home/dmm2017/cloudSPAdes-dev/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion to ‘gnu_cxx::alloc_traits<std::allocator
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Built target nlopt [ 19%] Built target ConsensusCore [ 29%] Built target BamTools [ 34%] Built target samtools [ 34%] Built target format [ 35%] Built target ssw [ 36%] Built target cityhash [ 37%] Built target getopt_pp [ 43%] Built target llvm-support [ 44%] Built target hattrie [ 48%] Built target bwa [ 49%] Built target gqf [ 50%] Built target edlib [ 50%] Built target gfa1 [ 59%] Built target spades-bwa [ 60%] Built target coverage_model [ 61%] Built target input [ 62%] Built target pipeline [ 63%] Built target sequence [ 66%] Built target assembly_graph [ 79%] Built target path_extend [ 80%] Built target modules [ 81%] Built target paired_info [ 82%] Built target stages [ 84%] Built target utils [ 84%] Built target mph_index [ 84%] Built target common_modules [ 85%] Built target graphio [ 89%] Built target spades-core [ 92%] Built target spades-hammer [ 96%] Built target spades-ionhammer [ 97%] Built target spades-dipspades-core [ 99%] Built target spades-corrector-core [ 99%] 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Hi @asl and @1dayac,
I'm using SPAdes 3.11.1 which was available in the cluster. However, I get err -11. Several of my assemblies stopped at the counting kmer step reporting only using 132 Mb of memory which makes me think that the problem is unrelated to memory.
I expected to solve this issue by compiling the source code (v3.13.1.tar.gz), but the compilation fails with a puzzling error 2.
params.txt spades.log compilation_spades_assembler.log
Any ideas on how to solve this?
Best wishes
Pablo
I expected to solve this issue by compiling the source code (v3.13.1.tar.gz), but the compilation fails with a puzzling error 2.
The error is:
/ceph/users/pgonzales/.conda/envs/testForNext/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
You need to have zlib installed. The configure seems to be picking the library from the conda env, but this won't work outside the environment.
I'm using SPAdes 3.11.1 which was available in the cluster. However, I get err -11. Several of my assemblies stopped at the counting kmer step reporting only using 132 Mb of memory which makes me think that the problem is unrelated to memory.
Yes. Most probably the problem is due to some I/O issues on your cluster.
I used a conda environment to try to compile SPAdes because cmake is not installed in the cluster and cmake failed to compile ("The C++ compiler does not support C++11 (e.g. std::unique_ptr)"). I'm planning to load the environment every time I launch SPAdes. I used conda install -c anaconda zlib in this environment and returned that all requested packages already installed. I'm now trying the SPAdes available through conda. So far it has gone beyond the kmer counting step and keeps going. If this doesn't work, I'll ask the cluster admins to help me compile it.
Thanks for the quick response pointing what was the compilation error and clarifying that compiling from source would be my the best bet.