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

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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 ...

    file ref_fasta

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

    bwa index "${ref_fasta}"

process bwa_mem {

    publishDir ...

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


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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:
    client_socket, address = sock.accept()
except socket.error, err:
    if err[0] == errno.EAGAIN:
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
#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

    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
      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 -- $!";

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
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