Hi I am having an error saying "Train dataset for temp stage can not filled. Branch training terminated. Cascade Classifier can't be trained. check the used training parameters" when I am trying to do training. I used 50 positive and 100 negative images. I saw a similar question here . My bg.txt file is already in the form mentioned in that solution but still having the error.
my console output was as follows-
C:\Users\Administrator\Documents\Visual Studio 2010\Projects\cv_traincascade
\Debug>cv_traincascade.exe -data test -vec positives.vec -bg infofile.txt -numPos 50 -
numNeg 100 -numStages 20 -precalcValBufSize 1024 -precalcIdxBufSize 1024 -w 24 -h 24
PARAMETERS:
cascadeDirName: test
vecFileName: positives.vec
bgFileName: infofile.txt
numPos: 50
numNeg: 100
numStages: 20
precalcValBufSize[Mb] :1024
precalcIdxBufSize[Mb] :1024
stageType: BOOST
featureType: HAAR
sampleWidth: 24
sampleHeight: 24
boostType: GAB
minHitRate: 0.995
maxFalseAlarmRate: 0.5
weightTrimRate: 0.95
maxDepth: 1
maxWeakCount: 100
mode: BASIC
===== TRAINING 0-stage =====
<BEGIN
POS count : consumed 50 : 50
Train dataset for temp stage can not be filled. Branch training terminated.
Cascade classifier can't be trained. Check the used training parameters.
Can anyone please say what is wrong in my command? any help will be appreciated. thank you.
You have a problem with your Background dataset, otherwise it would move through the Bg Count and start the classifier. Check the file locations are all correct in your background file "infofile.txt"
EDIT: Upload a portion of your bg file.
Related
I'm working on a Raspberry Pi running Buster with an Adafruit Ultimate GPS hat. I'm trying to get Chrony to temperature compensate. I've modified the chrony.conf file to contain.
# Uncomment the following line to turn logging on.
log measurements refclocks statistics tempcomp tracking
tempcomp /sys/class/hwmon/hwmon0/temp1_input 30 26000 0.0 0.000183 0.0
#tempcomp /sys/class/hwmon/hwmon0/temp1_input 30 /var/log/chrony/tempcomp.log
The system is currently adding measurements to the tempcomp.log file every 30 seconds. However, if I enable the second (commented out) tempcomp line above, chrony dies on restart with the error
Sep 6 12:31:45 rpi-tick2 chronyd[24713]: chronyd version 3.4 starting (+CMDMON +NTP +REFCLOCK +RTC +PRIVDROP +SCFILTER +SIGND +ASYNCDNS +SECHASH +IPV6 -DEBUG)
Sep 6 12:31:45 rpi-tick2 chronyd[24713]: Frequency 23.662 +/- 0.165 ppm read from /var/lib/chrony/chrony.drift
Sep 6 12:31:45 rpi-tick2 chronyd[24713]: Fatal error : Could not read tempcomp point from /var/log/chrony/tempcomp.log
Sep 6 12:31:45 rpi-tick2 chronyd[24711]: Could not read tempcomp point from /var/log/chrony/tempcomp.log
I believe this is due to the fact that the tempcomp.log files has entries like
===========================================
Date (UTC) Time Temp. Comp.
===========================================
2021-09-06 17:40:47 5.2095e+04 4.7754e+00
2021-09-06 17:41:17 5.2582e+04 4.8645e+00
2021-09-06 17:41:47 5.2582e+04 4.8645e+00
2021-09-06 17:42:17 5.3069e+04 4.9536e+00
2021-09-06 17:42:47 5.2582e+04 4.8645e+00
Where chrony is expecting something like
20000 1.0
21000 0.64
22000 0.36
23000 0.16
24000 0.04
and sorted by temperature not sample time.
So it seems like I'm missing a step somewhere.
Also, once set up, is this a dynamic process where new datapoints are added as we go, or do we stop collecting data and just use the static table to compensate for temps?
Thanks for any insights.
I think you have to manually create a chrony.tempcomp file, likely by analyzing the tempcomp.log file. They are separate files. Then specify the chrony.tempcomp file like this:
tempcomp /sys/class/hwmon/hwmon0/temp2_input 30 /etc/chrony.tempcomp
Hello everyone,
I have a bash file which has the following code:
./lda --num_topics 15 --alpha 0.1 --beta 0.01 --training_data_file testdata/test_data.txt --model_file Model_Files/lda_model_t15.txt --burn_in_iterations 120 --total_iterations 150
This works perfectly fine normally but when I run it in a cluster it is not loading the data that it is supposed to load from the connected .cc files. I have given #!/bin/bash in the header. What can I do to rectify this situation? Please help!
You will need to mention the full path to the lda executable. Since it's not invoked by you manually, the system will not know where to find the executable if invoked by the shell. Since this is not a shell command, you don't necessarily need the #!/bin/bash even.
/<FullPath>/lda --num_topics 15 --alpha 0.1 --beta 0.01 --training_data_file testdata/test_data.txt --model_file Model_Files/lda_model_t15.txt --burn_in_iterations 120 --total_iterations 150
I am running an executable in Condor that basically processes an input Image and saves a binary image in a given folder. I use this code in 213 images.
My condor configuration file contents are as following:
universe = vanilla
executable = /datasets/me/output_cpen_database/source_codes_techniques/test/vole
arguments = cmfd -I /datasets/me/cpen_database/scale1/$(Process)/$(Process).png -O /datasets/me/output_cpen_database/scale1/dct/$(Process)/ --numThreads 10 --chan GRAY --featvec DCT --blockSize 16 --minDistEuclidian 50 --kdsort --fastsats --minSameShift 1000 --markRegions --useOrig --writePost --writeMatrix
initialdir = /datasets/me/output_cpen_database/source_codes_techniques/test
requirements = (OpSysAndVer == "Ubuntu12")
request_cpus = 5
request_memory = 20000
output = logs/output-$(Process).log
error = logs/error-$(Process).log
log = logs/log-$(Process).log
Notification = Complete
Notify_User = mymail#gmail.com
Queue 214
Some images are processed OK, but in some cases I receive the following error in my mailbox:
Condor job 1273.47
/datasets/me/output_cpen_database/source_codes_techniques/test/vole cmfd -I /datasets/me/cpen_database/scale1/47/47.png -O /datasets/me/output_cpen_database/scale1/dct/47/ --numThreads 10 --chan GRAY --featvec DCT --blockSize 16 --minDistEuclidian 50 --kdsort --fastsats --minSameShift 1000 --markRegions --useOrig --writePost --writeMatrix
died on signal 9 (Killed)
I was thinking if this happens because of lack of memory, but this image's (named 47) size is not longer than 20MB (actually it has 16.7MB).
As I said before, the condor runs this executable ok for some other images .
Should I have to increase the request_memory in my configuration file? what is happening here?
Usually, a job dying on signal 9 means problems with some of the shared libraries required by your executable. What I would check is whether or not all jobs die on a particular host. If that's the case, you could run the code manually and see if you get a missing shared library error.
Need to recruit the help of any budding bioinformaticians that are lurking in the shadows here.
I am currently in the process of formatting some .fasta files for use in a set of grouping programs but I cannot for the life of me get them to work. First things first, all the files have to have a 3 or 4 character name such as the following:
PP41.fasta
PP59.fasta
PPBD.fasta
...etc...
The files must have headers for each gene sequence that look like so: >xxxx|yyyyyyyyyy where xxxx is the same 3 or 4 letter 'taxon' identifier as the file names I put above and yyyyyyy is a numerical identifier for each of the proteins within each of the taxons (the pipe symbol can also be replaced with an _ as below). I then cat all of these in to one file which has a header that looks correct like so:
>PP49_00001
MIENFNENNDMSDMFWEVEKGTGEVINLVPNTSNTVQPVVLMRLGLFVPTLKSTKRGHQG
EMSSMDATAELRQLAIVKTEGYENIHITGARLDMDNDFKTWVGIIHSFAKHKVIGDAVTL
SFVDFIKLCGIPSSRSSKRLRERLGASLRRIATNTLSFSSQNKSYHTHLVQSAYYDMVKD
TVTIQADPKIFELYQFDRKVLLQLRAINELGRKESAQALYTYIESLPPSPAPISLARLRA
RLNLRSRVTTQNAIVRKAMEQLKGIGYLDYTEIKRGSSVYFIVHARRPKLKALKSSKSSF
KRKKETQEESILTELTREELELLEIIRAEKIIKVTRNHRRKKQTLLTFAEDESQ*
>PP49_00002
MQNDIILPINKLHGLKLLNSLELSDIELGELLSLEGDIKQVSTGNNGIVVHRIDMSEIGS
FLIIDSGESRFVIKAS*
Next step is to construct a blast database which I do as follows, using the formatdb tool of NCBI Blast:
formatdb -i allproteins.fasta -p T -o T
This produces a set of files for the database. Next I conduct an all-vs-all BLAST of the concatenated proteins against the database that I made of them like so, which outputs a tabular file which I suspect is where my issues are beginning to arise:
blastall -p blastp -d allproteins.fasta -i allproteins.fasta -a 6 -F '0 S' -v 100000 -b 100000 -e 1e-5 -m 8 -o plasmid_allvall_blastout
These files have 12 columns and look like the below. It appears correct to me, but my supervisor suspects the error is in the blast file - I don't know what I'm doing wrong however.
PP49_00001 PP51_00025 100.00 354 0 0 1 354 1 354 0.0 552
PP49_00001 PP49_00001 100.00 354 0 0 1 354 1 354 0.0 552
PP49_00001 PPTI_00026 90.28 288 28 0 1 288 1 288 3e-172 476
PP49_00001 PPNP_00026 90.28 288 28 0 1 288 1 288 3e-172 476
PP49_00001 PPKC_00016 89.93 288 29 0 1 288 1 288 2e-170 472
PP49_00001 PPBD_00021 89.93 288 29 0 1 288 1 288 2e-170 472
PP49_00001 PPJN_00003 91.14 79 7 0 145 223 2 80 8e-47 147
PP49_00002 PPTI_00024 100.00 76 0 0 1 76 1 76 3e-50 146
PP49_00002 PPNP_00024 100.00 76 0 0 1 76 1 76 3e-50 146
PP49_00002 PPKC_00018 100.00 76 0 0 1 76 1 76 3e-50 146
SO, this is where the problems really begin. I now pass the above file to a program called orthAgogue which analyses the paired sequences I have above using parameters laid out in the manual (still no idea if I'm doing anything wrong) - all I know is the several output files that are produced are all just nonsense/empty.
Command looks like so:
orthAgogue -i plasmid_allvsall_blastout -t 0 -p 1 -e 5 -O .
Any and all ideas welcome! (Hope I've covered everything - sorry about the long post!)
EDIT Never did manage to find a solution to this. Had to use an alternative piece of software. If admins wish to close this please do, unless it is worth having open for someone else (though I suspect its a pretty niche issue).
Discovered this issue (of orthAgogue) first today:
though my reply may be old, I hope it may help future users;
issue is due to a missing parameter: seems like you forgot to specify the separator: -s '_', ie, the following set of command-line parameters should do the trick*:
orthAgogue -i plasmid_allvsall_blastout -t 0 -p 1 -e 5 -O -s '_'
(* Under the assumption that your input-file is a tabular-seperated file of columns.)
A brief update after comment made by Joe:
In brief, the problem described in the intiail error report (by Joe) is (in most cases) not a bug. Instead it is one of the core properties of the Inparanoid algorithm which orthAgogue implements: if your ortholog-result-file is empty (though constructed), this (in most cases) implies that there are no reciprocal best match between a protein-pair from two different taxa/species.
One (of many) explanations for this could be that your blastp-scores are too similar, a case where I would suggest a combined tree-based/homology clustering as in TREEFAM.
Therefore, when I receive your data, I'll send it to one of the biologists I'm working with, with goal of identifying the tool proper for your data: hope my last comment makes your day ;)
Ole Kristian Ekseth, developer of orthAgogue
what I want is to add eps file into temporary ps file which has text written, then I convert my ps file to eps file using ghostscript, but when I see my eps file in AI outline mode, I see extra square around my eps file which is size box, which should not be there, It should be part of single compound box
Ghostscript version is 9.05 and before I include eps into ps I need to resize it. So resized eps file shows page border into outline mode. Which is actually not there, but when it goes to machine it will cut out that path which should not be case.
Alright, I think I have some understanding of what you're doing and where the trouble may be creeping in. As I commented, you're running the file through ghostscript multiple times. Each time it has to interpret the postscript code and construct an internal display-list representation and then recreate appropriate postscript code on the output end. So it's the clone of a clone of a clone problem. Any little hiccup can cause cascade failures.
So, enough of being preachy. The alternative is to manipulate the eps file as text.
So, if we want the image to be scaled to fill a 500x500 square, we will be guided by the number in the BoundingBox comment. I'll quote this silly file from the linked question as an example:
%!PS-Adobe-2.0 EPSF-2.0
%%BoundingBox: 72 700 127 708 %<-- modify this
%%HiResBoundingBox: 72.000000 700.000000 127.000000 707.500000 %<-- delete this
%%EndComments
% EPSF created by ps2eps 1.68
%%BeginProlog
save
countdictstack
mark
newpath
/showpage {} def
/setpagedevice {pop} def
%%EndProlog
%%Page 1 1 %<-- insert translate and scale after this line
/Times-Roman findfont
11 scalefont setfont
72 700 moveto
(This is a test)show
%%Trailer
cleartomark
countdictstack
exch sub { end } repeat
restore
%%EOF
So, the BoundingBox was %%BoundingBox: 72 700 127 708 and it needs to be 0 0 500 500 or rather (to preserve the aspect ratio) 0 0 x 500 or 0 0 500 y where x or y (whichever it happens to be) is < 500. The existing size is 127-72 x 708 - 700 = 55 x 8. So our scaling factor is 500/55. But we also want to translate the lower-left corner to the origin, and its simplest to do that first, so the scaling doesn't affect the interpretation of the numbers.
So, to take 72 700 127 708 to 0 0 500 y, first we add -72 -700 translate to the file, and modify the bounding box to 0 0 55 8, and delete that silly HiRes line: we don't really need it.
Then, we add 500 55 div dup scale (let the interpreter do the math, hee hee). So the maximum x will now be 500, but, oh, what to put for the y? A quick calculation yields 72!
So, this awk program will modify an eps file to be 500 points wide, with y scaled appropriately.
/%%BoundingBox: ([^ ]*) ([^ ]*) ([^ ]*) ([^ ]*)/{x=$2;y=$3;w=$4-x;h=$5-y;print $1,0,0,500,(500/w)*h}
!/%%BoundingBox:/&&!/%%HiRes/{print}
/%%Page /{print -x,-y,"translate"; print 500,w,"div dup scale"}
Usage:
$ awk -f epsscale.awk etest.eps