Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
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isEmail function in run script makes Manta hang #293

Open holtgrewe opened 2 years ago

holtgrewe commented 2 years ago

I am using Manta v1.6.0. My manta workflow script runs hang. Running things through strace -f, I found the following.

socket(AF_INET, SOCK_STREAM, IPPROTO_TCP) = 3
connect(3, {sa_family=AF_INET, sin_port=htons(25), sin_addr=inet_addr("127.0.0.1")}, 16) = 0
recvfrom(3, 

The server (Rocky Linux 7) uses no firewall but also does not run an SMTP server.

I suggest changing the following

    def isLocalSmtp() :
        import smtplib
        try :
            smtplib.SMTP('localhost')
        except :
            return False
        return True

to

    def isLocalSmtp() :
        import smtplib
        try :
            smtplib.SMTP('localhost', timeout=2)
        except :
            return False
        return True

or similar.