liangwx332
commented
2 years ago I try to search the python module of pybionano.smapdata ,bur without any result. I do not know why does runBNG miss the module?
Open liangwx332 opened 2 years ago
liangwx332
commented
2 years ago I try to search the python module of pybionano.smapdata ,bur without any result. I do not know why does runBNG miss the module?
yuxuanyuan
commented
2 years ago Sorry for the late reply. You may download Bionanao Solve3.5.1 and try again.
Hello,
I run runBNG for your example and all dependence has been solved. But I did not get right result, the error as following. Would you give me some suggestions?
Lwx
========================= ============Code=================================== runBNG denovo -t /share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1/RefAligner/12432.12463rel/ -s /share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1/ -b Molecules.bnx -T 5 -l 120 -m 8 -j 30 -z 100 -o test
======================================Error=================================== ========================================== De novo assembly starts =============================================
The data generation platform is: saphyr
The bnx file is: /share/home/biosoft/runBNG-master/Examples/Molecules.bnx
The minimum molecule length is (Kb): 120
The minimum label on a molecule is: 8
Maximum backbone intensity is: 0.6
The path to Bionano Solve folder is: /share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1
The path to Bionano RefAligner folder is: /share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1/RefAligner/12432.12463rel
The number of threads is: 5
Large jobs maximum memory (GB) is: 128
Small jobs maximum memory (GB) is: 8
The number of threads for each subjob is: 30
The number of iterations is: 5
False Positive Density (/100Kb) [FP]: 2.0
False Negative Rate (%/100) [FN]: 0.10
ScalingSD (Kb^1/2) [sd]: 0.0
SiteSD (Kb) [sf]: 0.12
RelativeSD [sr]: 0.03
The genome size (Mb) is: 100
The xml file is: /share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1/RefAligner/12432.12463rel/optArguments_nonhaplotype_DLE1_saphyr.xml
The output directory is: test
Traceback (most recent call last): File "/share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1/Pipeline/1.0/pipelineCL.py", line 11, in
import Pipeline
File "/share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1/Pipeline/10192021/Pipeline.py", line 31, in
import reports
File "/share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1/Pipeline/10192021/reports.py", line 8, in
from varcluster import VariantClustering
File "/share/home/biosoft/tools/pipeline/Solve3.7_10192021_74_1/Pipeline/10192021/varcluster.py", line 7, in
from pybionano.smapdata import SmapData, SmapFilter
ModuleNotFoundError: No module named 'pybionano.smapdata'