Open dcopetti opened 5 years ago
Some more thoughts: I am using a single map made with the DLE chemistry, BspTI (CTTAAG) is the enzyme. The data was collected on Saphyr, the assembly run in BionanoAccess.
-m
is a text file with a single line looking like this:
BspTI /path/to/DNassembly/output/contigs/exp_refineFinal1/EXP_REFINEFINAL1.cmap
separated by a tab. If I separe the field by a space, but I get the same error. How should that field be separated?
I added "BspTI" => "CTTAAG"
to fa2cmap_multi.pl
, that runs normally.
Looking at the stdout file, I see that the header looks for BspQI:
# CMAP File Version: 0.1
# Label Channels: 1
# Nickase Recognition Site 1: GCTCTTC
# Enzyme 1: BspQI
# Number of Consensus Nanomaps: 184229
and it looks a bit different than the header of my .cmap file:
# hostname=saphyr1c
# $ cd /home/bionano; /home/bionano/tools/pipeline/1.0/RefAligner/1.0/RefAligner -if /home/bionano/access/local/jobs/1198184/output/contigs/curContigs -merge -o /home/bionano/access/local/jobs/1198184/output/contigs/exp_refineFinal1/EXP_REFINEFINAL1 -f -stdout -stderr
# CompileDir= /home/users4/tanantharaman/branches/7915/7915.7989rel/7915.7989rel CompileCmd=/opt/gcc-5.4.0/bin/g++ -B/opt/binutils-2.27 -fopenmp -Ofast -mavx2 -mfpmath=sse -DUSE_PFLOAT=1 -DUSE_RFLOAT=1 -DUSE_SSE=1 -DUSE_MFLOAT=1 -DUSE_EPOW=1 -I/opt/glibc-2.24/include -DUSE_STATIC -freciprocal-math -fno-signed-zeros -fno-trapping-math -DRELEASE=1 -std=gnu++98 -Wl,--dynamic-linker=/opt/glibc-2.24/lib/ld-linux-x86-64.so.2 -Wl,--rpath=/opt/glibc-2.24/lib -Wl,--rpath=/opt/gcc-5.4.0/lib64 -lrt -lmvec -L/opt/glibc-2.24/lib -L/opt/gcc-5.4.0/lib64 -static -s SVNversion=7989 $Header: http://svn.bnm.local:81/svn/Informatics/RefAligner/branches/7915/RefAligner.cpp 7959 2018-10-09 04:21:44Z tanantharaman $
# FLAGS: USE_SSE=1 USE_AVX=1 USE_MIC=0 USE_PFLOAT=1 USE_RFLOAT=1 USE_MFLOAT=1 USE_EPOW=1 DEBUG=1 VERB=1
# CMAP File Version: 0.2
# Label Channels: 1
# Nickase Recognition Site 1: cttaag;green_01
# Number of Consensus Maps: 268
did you try running Chimericognizer on a map made with DLE chemistry and assembled on BionanoAccess?
There you go, from the last line of output_1/refaligner/input_contigs_BspTI_BNG_VS_seq.stdout :
CMAP File Version 0.2 in /home/copettid/lolium_bionano/BNaccess_outputs/DN_1198184_250_12/output/contigs/exp_refineFinal1/EXP_REFINEFINAL1.cmap not supported (Only 0.1 is supported)
but this still does not explain why the test run fails.
any clue?
Hi Dario, Thanks for your interest. I carefully read the error information you provide, but I haven't figured out how could these errors happen. Refaligner is a C++ executable provided by Bionano company, and I use os.system() to run it in my python script, which means the running of Refaligner should not be related with python. So I have no idea why the error information ask you to look at some python document for details. Seems the system is looking at each line of Refaligner executable, which is also weird to me. If you want to check if the Refaligner is working on you computer, you could run it independently without Chimericognizer.
Weihua
Hi, Running RefAligner directly tells me this:
$ ./RefAligner
# hostname=kp141-242
# $ cd /home/copettid/bin/Bionano_tools_AVX; ./RefAligner
# CompileDir= /home/users3/tanantharaman/branches/4794/4794.5122/4794.5122 CompileCmd=/opt/gcc-4.9.2TSAN/bin/g++ -fopenmp -Ofast -fno-associative-math -mavx -mfpmath=sse -DUSE_PFLOAT=1 -DUSE_RFLOAT=1 -DUSE_SSE=1 -I/home/users/tanantharaman/amdlibm-3-0-2/include -DREPLACE_WITH_AMDLIBM -DUSE_STATIC -flto -DRELEASE=1 -lrt -L/home/users/tanantharaman/amdlibm-3-0-2/lib/static -lamdlibm -L/opt/gcc-4.9.2TSAN/lib64 -s -static SVNversion=5122 $Header: http://svn.bnm.local:81/svn/Informatics/RefAligner/branches/4794/RefAligner.cpp 4916 2016-05-10 18:12:38Z kbhakta $
# FLAGS: USE_SSE=1 USE_AVX=1 USE_MIC=0 USE_PFLOAT=1 USE_RFLOAT=1 DEBUG=1 VERB=1
No map input file specified: only -merge supported with null input map set
Can you confirm that Chimericognizer should work also with v2 cmap files? I am in contact with Bionano support as well, let's see what they say. Thanks!
hi @pwhhero Do you have any update on this issue? Can it be that the Chimericognizer scripts work only with the first version of the Bionano HS output files? Thanks, Dario
Hi @dcopetti I had the same problem here. You should upgrade RefAligner to the latest version. Should work
Hello, I was able to install Chimericognizer and the dependencies, though RefAligner is giving me a problem. I downloaded the AVX version (as suggested here), and when I run Chimericognizer with the test data, I get this error:
If I run with my own data, I get this error, pointing again that RefAligner folder is missing:
Is there any other step I am missing about how to install it? I am running it on a Fedora v28 OS, but I get the same error also on a CentOS v7 with Python 2.7.5. Thanks, Dario