A modular single-molecule analysis interface

When I try to filter Chimera data to lower frequencies (<500kHz) with the filter order too high (8 for 500kHz but even at 4 for 250kHz and below) MOSAIC generates artificial events that are not seen in the raw data (see attached images). These events are very frequent (>50/s) and are spaced in multiples of 2.4ms so I am assuming it is some sort of chunking of the data that messes up the filter. My current blocksizeSec is set to 0.1 so that is way higher than the spacing of these events I am seeing.

All of these events have the same general shape which looks like this one: Clearly not a real translocation event.

I plotted the difference of the absolute start times of the first 100 events to make clear that they are spaced evenly.

I am using the besselLowpassfilter for all of this

Solid-state nanopores often change size over the course of a few hours of current data, making the values of baseline stats calculated at the beginning in applicable to later sections of the same run. An option that allows calculation of local baseline for each new chunk of data requested would be helpful for analysis of long solid-state nanopore runs.

If the histogram built by ionic current stats contains a large number of zeros, fitting will fail and give enormous values for perr. The solution is simple: weight the residuals by the y values. You can see an explanation here:

http://math.stackexchange.com/questions/1771660/analytical-solution-to-nonlinear-least-squares-problem

I'm not 100% sure how to fit this intro curve_fit, however. They provide a sigma parameter, which weights data points as 1/sigma^2, so it get y-weighting you would have to provide sigma=1/sqrt(y), which is undefined for y=0. I think the proper solution would be to use scipy.optimize.minimize directly and write a custom residuals function.

Issue: After activating the "stop analysis" button on the GUI the system runs extremely slow.

I first looked at the Ubuntu user processes using the command, ~$ ps -u

Steps to Replicate Problem:

While running MOSAIC and analysing a file the user processes looks like this:

hiyomika@ubuntu:~$ ps -u
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
hiyomika  2895  0.0  0.0  27836  4016 pts/11   Ss   12:40   0:00 bash
hiyomika  3271  0.0  0.0  27664  3372 pts/0    Ss   12:43   0:00 bash
hiyomika  6821 11.5 26.1 2694768 1056896 pts/11 Sl+ 14:33   0:07 python mosaicgui/mosaicGUI.py
hiyomika  6872 71.7 48.1 3613440 1945972 pts/11 R+  14:34   0:06 python mosaicgui/mosaicGUI.py
hiyomika  6880  0.0  0.0  22644  1292 pts/0    R+   14:34   0:00 ps -u

The program is running like it is suppose too. After hitting the Stop Analysis button the processes look like this.

hiyomika@ubuntu:~$ ps -u
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
hiyomika  2895  0.0  0.1  27836  4964 pts/11   Ss   12:40   0:00 bash
hiyomika  3013  9.4 27.1 2276980 1098748 pts/11 Sl+ 12:40   0:21 python mosaicgui/mosaicGUI.py
hiyomika  3229 96.5  0.0      0     0 pts/11   Z+   12:43   1:29 [QThread] <defunct>
hiyomika  3271  0.0  0.1  27660  4644 pts/0    Ss   12:43   0:00 bash
hiyomika  3361  0.0  0.0  22644  1292 pts/0    R+   12:44   0:00 ps -u

The second thread responsible for the analysis of the file does not clear out while maintaining a high CPU percentage.

After refreshing the processes list we see the amount of CPU the defunct thread takes up lessens to almost nothing.

hiyomika@ubuntu:~$ ps -u
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
hiyomika  2895  0.0  0.1  27836  4740 pts/11   Ss   12:40   0:00 bash
hiyomika  3271  0.0  0.1  27660  4520 pts/0    Ss   12:43   0:00 bash
hiyomika  3377  5.7 25.9 2306092 1047720 pts/11 Sl+ 12:45   4:37 python mosaicgui/mosaicGUI.py
hiyomika  3772  0.1  0.0      0     0 pts/11   Z+   12:52   0:08 [QThread] <defunct>
hiyomika  5970  0.0  0.0  22644  1292 pts/0    R+   14:05   0:00 ps -u

Good news is if you start another analysis run the defunct thread is replaced with a working thread.

Direct Symptoms: Expect system to run slow immediately after cancelling an analysis run.

Current Work Around: Close Program out and initialize to clear out the non working thread.

Update: When a file is allowed to continue unto completion the thread correctly clears. As shown below.

hiyomika@ubuntu:~$ ps -u
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
hiyomika  2895  0.0  0.0  27836  4016 pts/11   Ss   12:40   0:00 bash
hiyomika  3271  0.0  0.0  27664  3372 pts/0    Ss   12:43   0:00 bash
hiyomika  6821 14.1 15.6 2273348 630608 pts/11 Rl+  14:33   1:35 python mosaicgui/mosaicGUI.py
hiyomika  7232  0.0  0.0  22644  1292 pts/0    R+   14:44   0:00 ps -u

Recently, when I tried to extract one of the events from the metadata (sqlite database), I found that the time series in the event was downsampled by almost a factor of 30. I have 15000 samples for the same event in my signal, but the extract from metadata has only 499 samples. The shape of the event's waveform is preserved. Both of them look exactly the same.

Incorporate chimeraTrajIO data reads into the webgui. Ideally this should include automatic .settings file creation by importing parameters from the corresponding .mat files

Hi, I am a novice and learning Mosaic. Here is a question about the exporting data of resident time and blockade current. How to export the the acquisition data of resident time and blockade current by using Mosaic. Thank you.

Since the relaxation that RC constants need not be equal in stepResponseAnalysis, a file I recently analyzed (available on request) had several events with negative RC constant for the second one but reported normal processing status.

When loading up data files generated by the Chimera VC100, the files are not loaded in the same order as they were generated. This messes up the time ordering in the overall current trace.

Currently I believe MOSAIC is set to abort analysis of the open channel current drifts past a defined threshold. Often it is the case that a clogged pore can be unclogged and the baseline would return to normal. It might be preferable to have mosaic continue processing data if the open channel current drifts significantly, but not look for events again until the current has returned to the initial state. This way you can ignore clogs and channel gating without missing out on analyzing data after the first clog, or having to chop the file into pieces to process it fully.

Adaptive CUSUM threshold implementation for testing. CUSUM now requires two threshold settings (MinThreshold and MaxThreshold) in order to function. Actual threshold used changes for each event and is stored in the DB.

With present MOSAIC package analysis, the rejected events have their start time as -1. But I want to have the time information for these events. I want to implement only an event detection module, independent of the event processing, and get the metadata for all the detected events including the start time.

Describe the bug A clear and concise description of what the bug is. Mosaic version 2.2 can not be executed in chrome or safari To Reproduce

• Device: [MacBook Pro 14 ]
• OS: [e.g. macOS monterey 12.1]
• Browser [e.g. safari or chorme]
• Version [e.g. mosaic2.2]

Additional context Add any other context about the problem here.

Describe the bug A clear and concise description of what the bug is.

To Reproduce Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior A clear and concise description of what you expected to happen.

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [e.g. iOS]
• Browser [e.g. chrome, safari]
• Version [e.g. 22]

Smartphone (please complete the following information):

• Device: [e.g. iPhone6]
• OS: [e.g. iOS8.1]
• Browser [e.g. stock browser, safari]
• Version [e.g. 22]

Additional context Add any other context about the problem here. Translated Report (Full Report Below)

Process: MOSAIC [9856] Path: /Applications/MOSAIC.app/Contents/MacOS/MOSAIC Identifier: MOSAIC Version: 1.3.6 (???) Code Type: X86-64 (Translated) Parent Process: launchd [1] User ID: 501

Date/Time: 2021-12-06 10:44:02.3937 +0800 OS Version: macOS 12.0.1 (21A559) Report Version: 12 Anonymous UUID: 8E4955EF-B107-0CB6-643D-06BB10BBA547

Sleep/Wake UUID: 5B89FCF5-94C7-4F97-B7A8-C64820B92F7B

Time Awake Since Boot: 8200 seconds Time Since Wake: 2349 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_INSTRUCTION (SIGILL) Exception Codes: 0x0000000000000001, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY

Termination Reason: Namespace SIGNAL, Code 4 Illegal instruction: 4 Terminating Process: exc handler [9856]

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 QtCore 0x112b52fa2 normalizeTypeInternal(char const*, char const*, bool, bool) + 792 1 QtCore 0x112b5036b qNormalizeType(char*, int&, QByteArray&) + 146 2 QtCore 0x112b5017b QMetaObject::normalizedType(char const*) + 211 3 QtCore 0x112b53d45 QMetaType::registerType(char const*, void ()(void), void* ()(void const)) + 93 4 PyQt4.QtCore.so 0x1121ab3f6 int qRegisterMetaType<PyQt_PyObject>(char const*, PyQt_PyObject*) + 47 5 PyQt4.QtCore.so 0x1121ab253 qpycore_post_init(object*) + 291 6 .Python 0x110fc1758 PyImport_LoadDynamicModule + 140 7 .Python 0x110fc11ef imp_load_module + 243 8 .Python 0x110fac53a PyEval_EvalFrameEx + 27019 9 .Python 0x110fa59bf PyEval_EvalCodeEx + 1618 10 .Python 0x110f4b088 function_call + 350 11 .Python 0x110f2ce95 PyObject_Call + 99 12 .Python 0x110f37b67 instancemethod_call + 173 13 .Python 0x110f2ce95 PyObject_Call + 99 14 .Python 0x110f2d023 call_function_tail + 72 15 .Python 0x110f2d21c PyObject_CallMethod + 231 16 .Python 0x110fc0454 import_submodule + 267 17 .Python 0x110fc0028 load_next + 280 18 .Python 0x110fbf240 PyImport_ImportModuleLevel + 1185 19 .Python 0x110fa0fbd builtin___import + 135 20 .Python 0x110f2ce95 PyObject_Call + 99 21 .Python 0x110fafb2b PyEval_CallObjectWithKeywords + 165 22 .Python 0x110faace3 PyEval_EvalFrameEx + 20788 23 .Python 0x110fa59bf PyEval_EvalCodeEx + 1618 24 .Python 0x110fa5367 PyEval_EvalCode + 48 25 MOSAIC 0x104b7f0c9 0x104b7d000 + 8393 26 MOSAIC 0x104b7f69a 0x104b7d000 + 9882 27 MOSAIC 0x104b7dec4 0x104b7d000 + 3780

Thread 1:: com.apple.rosetta.exceptionserver 0 runtime 0x7ff7ffca08e4 0x7ff7ffc9c000 + 18660 1 runtime 0x7ff7ffcad928 0x7ff7ffc9c000 + 71976 2 runtime 0x7ff7ffcaf0a4 0x7ff7ffc9c000 + 77988

Thread 2: 0 runtime 0x7ff7ffcbe814 0x7ff7ffc9c000 + 141332

Thread 3: 0 runtime 0x7ff7ffcbe814 0x7ff7ffc9c000 + 141332

Thread 4: 0 runtime 0x7ff7ffcbe814 0x7ff7ffc9c000 + 141332

Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000025 rbx: 0x000000030e6cee18 rcx: 0x0000000000000000 rdx: 0x0000000000000008 rdi: 0x0000000112be525b rsi: 0x000000030e6cee18 rbp: 0x000000030e6cedb0 rsp: 0x000000030e6cece0 r8: 0x0000000000000050 r9: 0x0000000000000074 r10: 0x00007ff854192b68 r11: 0x0000000110fdb238 r12: 0x000000030e6cee25 r13: 0x000000000000000d r14: 0x0000000112cc7a68 r15: 0x000000030e6cee18 rip: 0x0000000112b52fa2 rfl: 0x0000000000000203 tmp0: 0x0000000112b52fa2 tmp1: 0x4429fcc5c057fcc5 tmp2: 0x00244429fcc56024

Binary Images: 0x112a47000 - 0x112cbdfff QtCore () <2878eedc-9ce1-3944-9514-c858d0d82326> /Applications/MOSAIC.app/Contents/MacOS/QtCore 0x1121a9000 - 0x1122fefff PyQt4.QtCore.so () <5b5264e0-aac9-338d-be10-a6843cf0893a> /Applications/MOSAIC.app/Contents/MacOS/PyQt4.QtCore.so 0x110f22000 - 0x111017fff .Python () <9a53817f-2101-3965-9831-1db81d851fba> /Applications/MOSAIC.app/Contents/MacOS/.Python 0x104b7d000 - 0x104b83fff MOSAIC (1.3.6) <32ab4b3f-56df-3c81-b3ee-2215ac410955> /Applications/MOSAIC.app/Contents/MacOS/MOSAIC 0x7ff7ffc9c000 - 0x7ff7ffccbfff runtime () <9f5d65be-d8d0-3979-bb05-e651a67e785c> /usr/libexec/rosetta/runtime

External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0

VM Region Summary: ReadOnly portion of Libraries: Total=882.7M resident=0K(0%) swapped_out_or_unallocated=882.7M(100%) Writable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)

                            VIRTUAL   REGION 

REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Activity Tracing 256K 1 Kernel Alloc Once 8K 1 MALLOC 206.1M 24 MALLOC guard page 96K 4 MALLOC_MEDIUM (reserved) 480.0M 4 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) Rosetta Arena 4096K 2 Rosetta Generic 1008K 249 Rosetta IndirectBranch 192K 2 Rosetta JIT 128.0M 1 Rosetta Return Stack 80K 8 Rosetta Thread Context 80K 8 STACK GUARD 12K 3 Stack 9772K 4 Stack Guard 56.0M 1 VM_ALLOCATE 17.3M 65 __DATA 15.5M 273 __DATA_CONST 8557K 144 __DATA_DIRTY 310K 80 __FONT_DATA 4K 1 __LINKEDIT 708.5M 44 __OBJC_RO 81.6M 1 __OBJC_RW 3120K 2 __TEXT 174.2M 283 __UNICODE 588K 1 dyld private memory 1024K 1 mapped file 5.0G 400 shared memory 800K 12 unshared pmap 2288K 2 =========== ======= ======= TOTAL 7.3G 1622 TOTAL, minus reserved VM space 6.4G 1622

Full Report

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], "experiments" : [

] } }

Model: MacBookPro18,3, BootROM 7429.41.5, proc 10:8:2 processors, 16 GB, SMC Graphics: Apple M1 Pro, Apple M1 Pro, Built-In Display: Color LCD, 3024 x 1964 Retina, Main, MirrorOff, Online Memory Module: LPDDR5 AirPort: Wi-Fi, wl0: Sep 24 2021 15:49:44 version 20.10.853.23.8.7.106 FWID 01-78e271b2 Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports Network Service: Wi-Fi, AirPort, en0 USB Device: USB31Bus USB Device: USB31Bus USB Device: USB3.0 Hub USB Device: USB 10/100/1000 LAN USB Device: Elements SE 2623 USB Device: USB2.0 Hub USB Device: USB 2.0 Hub USB Device: USB Receiver USB Device: USB Billboard Device USB Device: USB31Bus Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc.

It would be useful to have a "remarks" field in the SQLite database that allows events to be tagged with user data, e.g. a voltage or buffer conditions that may change between files or even within a file.

Alternatively, the database could contain additional fields for "settings" values that aren't otherwise used.

Problem: When using GUI to analyze a very long data set (time series written out), gui stalled. Error suggests problem writing to database. This error occurred after ~100k events written out. (total size of db was ~500MB). To my knowledge, user was not manually updating the BD histogram when this error occurred. Commit Version: 53e7a14499bb517b0be063c1b73031a6cc9c2545

Notes Is it possible this problem is due to the processing thread and GUI trying to access the database at the same time? As the number of events gets large the query time for the BD histogram increases.

Console output:

Traceback (most recent call last):
  File "/Users/hnw5/Projects/mosaic/mosaicgui/fiteventsview/fiteventsview.py", line 254, in OnEventIndexLineEditChange
    self.eventIndex=int(self.eventIndexLineEdit.text())
ValueError: invalid literal for int() with base 10: ''

Traceback (most recent call last):
  File "/Users/hnw5/Projects/mosaic/mosaicgui/fiteventsview/fiteventsview.py", line 254, in OnEventIndexLineEditChange
    self.eventIndex=int(self.eventIndexLineEdit.text())
ValueError: invalid literal for int() with base 10: ''
database is locked
database is locked

Process Process-1:
Traceback (most recent call last):
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/hnw5/Projects/mosaic/mosaic/apps/SingleChannelAnalysis.py", line 42, in run_eventpartition
    EventPartition.PartitionEvents()
  File "/Users/hnw5/Projects/mosaic/mosaic/partition/metaEventPartition.py", line 198, in PartitionEvents
    self._writeanalysisinfo()
  File "/Users/hnw5/Projects/mosaic/mosaic/partition/metaEventPartition.py", line 296, in _writeanalysisinfo
    self.FsHz
  File "/Users/hnw5/Projects/mosaic/mosaic/mdio/sqlite3MDIO.py", line 170, in writeAnalysisInfo
    self.db.execute( 'INSERT INTO analysisinfo VALUES(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)',  (infolist+[mosaic.__version__, mosaic.__build__, None]))
OperationalError: database is locked
^C^CTraceback (most recent call last):
  File "/Users/hnw5/Projects/mosaic/mosaicgui/statisticsview/statisticsview.py", line 251, in OnAppIdle
    def OnAppIdle(self):
KeyboardInterrupt