logo
down
shadow

Issue with bwa mem process not running on all output files from previous process


Issue with bwa mem process not running on all output files from previous process

Content Index :

Issue with bwa mem process not running on all output files from previous process
Tag : development , By : Jorge Palacio
Date : January 12 2021, 07:00 PM

wish help you to fix your issue Yes - Basically it's better to avoid splitting your fasta file into multiple channels and just use a single value which is implicitly a value channel:
ref_fasta = file(params.fasta)

process build_bwa_index {

    storeDir ...

    input:
    file ref_fasta

    output:
    file "*.{amb,ann,bwt,pac,sa}" into bwa_index

    """
    bwa index "${ref_fasta}"
    """
}

process bwa_mem {

    publishDir ...

    input:
    set name, file(reads) from trimmed_fastq
    file ref_fasta
    file "*" from bwa_index

    ...
}

Comments
No Comments Right Now !

Boards Message :
You Must Login Or Sign Up to Add Your Comments .

Share : facebook icon twitter icon

why a new process entry then the events of old process stop running when sharing a listening socket for multiple process


Tag : python , By : Keonne Rodriguez
Date : March 29 2020, 07:55 AM
With these it helps I think that the problem is in your code, because this code is working fine, with the same shared socket.
When you accept sa ocket with EV_READ, you must get the client socket and free the control over the main socket; you must not write to it. You should use code similar to the following one:
try:
    client_socket, address = sock.accept()
except socket.error, err:
    if err[0] == errno.EAGAIN:
        sys.exc_clear()
        return
    raise
core.event(core.EV_READ, client_socket.fileno(), callback)
core.event(core.EV_WRITE, client_socket.fileno(), callback)
core.event(core.EV_READ | core.EV_WRITE, client_socket.fileno(), callback)

Run a commandline process and get the output while that process is still running?


Tag : .net , By : Revision17
Date : March 29 2020, 07:55 AM
seems to work fine I think there may be bugs in dbPowerAmp's encoding. The output looks great in a cmd.exe /u Unicode environment, but it seems when you hook up a .Net Process object, it ends up with null bytes in between characters. You can work around this by discarding null bytes in between good UTF8 characters.
I'm more fluent in PowerShell, so here's what I wrote to prove that this will work.
$progressCounter = 0.0
$progressScaleString = "0%-----------25%-----------50%-----------75%-----------100%"
$psi = new-object system.diagnostics.processstartinfo
$psi.FileName = "C:\Program Files (x86)\Illustrate\dBpoweramp\CoreConverter.exe"
# Moby Dick audiobook available at <http://ia600208.us.archive.org/0/items/moby_dick_librivox/mobydick_135_melville.mp3>
$psi.arguments =  '-infile="C:\AudioBooks\mobydick_135_melville.mp3" -outfile="c:\AudioBooks\mobydick_135_melville.flac" -convert_to="flac" -encoding="SLOW"'
$psi.StandardOutputEncoding = [System.Text.Encoding]::Unicode
$psi.RedirectStandardOutput = $true
$psi.UseShellExecute = $false
$proc = new-object System.Diagnostics.Process
$proc.StartInfo = $psi
$proc.Start();
#Look for the magic progress bar string
$outputBuf = ""
while($true){ $chr = [char]$proc.StandardOutput.BaseStream.ReadByte(); if($chr -ne [char]0){ $outputBuf += $chr; } if($outputBuf.Contains($progressScaleString)){ break; }else{ sleep .01; }}
#We've seen the progress ruler, now start counting the pips.
while($progressCounter -le 100.0){ $chr = $proc.StandardOutput.BaseStream.ReadByte(); if($chr -lt 0){break;} if([char]$chr -eq [char]"*"){ $progressCounter += 100.0/($progressScaleString.Length+1); write-host $progressCounter; }}
Public Event PercentDone(ByVal Percent As Float)

Private Shared CoreConverter As New Process()

Private Shared CoreConverter_Info As New ProcessStartInfo() With { _
              .CreateNoWindow = True, _
              .UseShellExecute = False, _
              .RedirectStandardOutput = True, _
              .RedirectStandardError = True _
}

Private Shared Sub Run_CoreConverter()

    Dim ProgressScaleString As String = "0%-----------25%-----------50%-----------75%-----------100%"
    Dim ProgressCounter As Float = 0.0

    CoreConverter_Info.FileName = "C:\CoreConverter.exe"
    CoreConverter_Info.Arguments = String.Format("-infile=""{0}"" -outfile=""{1}"" -convert_to=""mp3 (Lame)""" ..., blah blah blah)
    CoreConverter_Info.StandardErrorEncoding = System.Text.Encoding.Unicode
    CoreConverter_Info.StandardOutputEncoding = System.Text.Encoding.Unicode
    CoreConverter.StartInfo = CoreConverter_Info
    CoreConverter.Start()

    Dim OutputBuf As String = ""
    Dim chr As Byte;
    While True
      chr = CoreConverter.StandardOutput.BaseStream.ReadByte();
      If chr < 0 Then
        Exit While
      ElseIf chr <> 0
        OutputBuf += CType(chr, Char)
      End If
      If OutputBuf.Contains(ProgressScaleString) Then
        Exit While
      Else
        System.Threading.Thread.Sleep(10)
      End If
    End While

    While ProgressCounter <= 100
      chr = CoreConverter.StandardOutput.BaseStream.ReadByte()
      If chr <= 0 Then
        Exit While
      End If
      If chr == CType("*"C, Char) Then
        ProgressCounter += 100.0/($progressScaleString.Length+1)
        RaiseEvent PercentDone(ProgressCounter)
      End If
    End While

End Sub

Running a PythonScript as a process and reading Standard Output issue


Tag : chash , By : stu73
Date : March 29 2020, 07:55 AM
may help you . Turns out the format I was passing in was wrong. I was using Postman REST Api client, and pasting the huge amounts of data into their request content window truncated it, leaving me with half a line. Once this was sorted, everything ran through ok.

How to wait for running process to complete in perl when running process is not child process?


Tag : perl , By : Brian
Date : March 29 2020, 07:55 AM
I think the issue was by ths following , Note   A simple-minded one-liner with kill 0, $pid is at end, commented.
ps --no-headers -o cmd PID
ps --no-headers -p PID -o cmd
use warnings;
use strict;

# For testing. Retrieve your PID as appropriate for real use    
my $ext_pid = $ARGV[0] || $$;

my $cmd_get_name = "ps --no-headers -o cmd $ext_pid";

# For testing.  Replace 'sleep' by your program name for real use
my $known_prog_name = 'sleep';

# Get the name of the program with PID
my $prog_name = qx($cmd_get_name);

# Test against the known name, exit if there is a mismatch
if ($prog_name !~ $known_prog_name) {
    warn "Mismatch between:\n$prog_name\n$known_prog_name -- $!";
    exit;
}   

my $name;
while ( $name = qx($cmd_get_name) and $name =~ /$prog_name/ )
{
    print "Sleeping 1 sec ... \n";
    sleep 1;
}   
# regex above may need slight adjustment, depending on format of ps return
sleep 30 &
script.pl `ps aux | egrep '[s]leep'`
while ( kill 0, $ext_pid ) { sleep 1 }

PowerShell, stream Process output and errors while running external process


Tag : powershell , By : Martin Kopp
Date : March 29 2020, 07:55 AM
Related Posts Related QUESTIONS :
  • "Objects are not valid as a React child" Redux error when conditionally connecting a component?
  • Displacy results are not showing
  • Strapi / Graphql. What am i doing wrong?
  • How to add Search bar for django template?
  • lookup in presto using single column against a range in lookup table
  • How can you stop videos being stolen on website?
  • Can't code substitution happen in Hybrid Flow?
  • Removed widget remains on parent
  • setup saga middleware with redux-starter-kit's configureStore()
  • How to get cookies from response of scrapy splash
  • I need to do a firebase stream and not a Http Get
  • Unable to compile node-runtime
  • SQLSTATE[42S22]: Column not found: 1054 Unknown column '' in 'where clause'
  • How to extract only the number from a variable
  • disable linter in DAML studio
  • RxJS: How to set exhaustMap concurrent?
  • How to remove perforce (p4) on Ubuntu
  • How do they know mean and std, the input value of transforms.Normalize
  • Why this type is not an Interface?
  • SugarCRM Rest API set_relationship between Contacts and Documents
  • Jira dashboard organization
  • Web worker importScripts fails to place script variables in global scope
  • Always errors - The "path" argument must be one of type string, Buffer, or URL. Received type undefined
  • How to create an observable of a stream of infinite items
  • Not efficiently to use multi-Core CPU for training Doc2vec with gensim
  • webGL gl_Position value saving outside shaders
  • Is it okay for a resolver to have side effects besides resolving the type?
  • Move 32bit register into a 8 bit register
  • Is there a way to update, not overwrite, worker_env for a Dask YarnCluster within a script?
  • Lotus Notes Deployment
  • How Do I Add Active Directory To APIM Using Terraform?
  • How to get the old parameter values in Blazor OnParameterSet?
  • How to debug "ERROR: Could not reach the worker node."?
  • How chain indefinite amount of flatMap operators in Reactor?
  • extract dates and times from string in Redshift
  • How do I make a column of 3 cards match in height in bootstrapVue?
  • how to replace missing values from another column in PySpark?
  • only read last line of text file (C++ Builder)
  • Snakemake --forceall --dag results in mysterius Error: <stdin>: syntax error in line 1 near 'File' from Graphvis
  • How Can I Remove Demo Products From APIM Created With Terraform?
  • How to avoid cloning a big integer in rust
  • Break a row of words into word groups in Hive
  • How can I add a path variable to existing files in an Installshield project converted from MSI
  • Certain languages are not available in postman; is there a way to enable it?
  • Concatenation step of U-Net for unequal number of channels
  • HL Fabric - states, transactions but varied keys
  • How to handle "flood wait" errors when using telethon.sync?
  • Any way to make closure which takes a destructured array?
  • What is the Difference between @PeculiarVentures 's `webcrypto` and `node-webcrypto-ossl`?
  • DWG Sheet Combination failing on AutoDesk Forge
  • karate.log(args) on afterScenario hook is not embedded on surefire json file
  • How do I output latest distinct values of specific fields and all other colums?
  • Clarification on lit-element components and where to browse them
  • Will websockets over HTTP2 also be multiplexed in streams?
  • How to apply switch statement for multi columns in datatables
  • frobot framework - Usage outside testing
  • How do I build against the UCRT with mingw-w64?
  • How to use someClass.android.ts and someClass.ios.ts without errors
  • ADB Connection to Samsung smart tv
  • is there a way to 2 create multiple command files in cypress
  • shadow
    Privacy Policy - Terms - Contact Us © scrbit.com