These are chat archives for dereneaton/ipyrad

17th
Dec 2018
Isaac Overcast
@isaacovercast
Dec 17 2018 15:59
@tle003 Try this: vdb-config -p. What does this return? What is the full path of the directory your notebook is running in?
@tle003 What does this return: esearch -db sra -query SRP021469?
jonatanleo
@jonatanleo
Dec 17 2018 16:17

hi @isaacovercast
I use ipyrad [v.0.7.28] and want to include [28] pop_assign_file in my parameter file, but it seems like ipyrad still reads the [24] min_samples_locus setting. I don't know if i have written my pop_assign_file in an unreadable way or if I have missed something else.

...
10455_8_1 easia
10455_16_2 easia
10455_25_2 easia
10455_31_1 easia
10456_38_1 easia
10456_41_1 easia
10456_43_1 easia
10456_50_1 easia
10468_13_1 easia
10468_22_1 easia
10468_33_1 easia
10468_45_2 easia

masia:4 nord:4 easia:4

Thank you!

tle003
@tle003
Dec 17 2018 16:20

@isaacovercast When I enter the esearch command I get:501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)
No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=SRP021469&retmax=0&usehistory=y&edirect_os=linux&edirect=10.2&tool=edirect&email=ubuntu@practice2'
Result of do_post http request is
$VAR1 = bless( {
'_content' => 'LWP will support https URLs if the LWP::Protocol::https module
is installed.
',
'_msg' => 'Protocol scheme \'https\' is not supported (LWP::Protocol::https not installed)',
'_headers' => bless( {
'client-warning' => 'Internal response',
'::std_case' => {
'client-date' => 'Client-Date',
'client-warning' => 'Client-Warning'
},
'content-type' => 'text/plain',
'client-date' => 'Mon, 17 Dec 2018 16:20:03 GMT'
}, 'HTTP::Headers' ),
'_request' => bless( {
'_uri' => bless( do{(my $o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi')}, 'URI::https' ),
'_headers' => bless( {
'content-type' => 'application/x-www-form-urlencoded',
'user-agent' => 'libwww-perl/6.15'
}, 'HTTP::Headers' ),
'_method' => 'POST',
'_content' => 'db=sra&term=SRP021469&retmax=0&usehistory=y&edirect_os=linux&edirect=10.2&tool=edirect&email=ubuntu@practice2'
}, 'HTTP::Request' ),
'_rc' => 501
}, 'HTTP::Response' );

WebEnv value not found in search output - WebEnv1

tle003
@tle003
Dec 17 2018 16:26
<The vdb-config -p command returns<Config>>
<APPNAME>vdb-config</APPNAME>
<APPPATH>/mnt/</APPPATH>
<AWS/>
<BUILD>RELEASE</BUILD>
<HOME>/home/ubuntu</HOME>
<HOST/>
<NCBI_HOME>/home/ubuntu/.ncbi</NCBI_HOME>
<NCBI_SETTINGS>/home/ubuntu/.ncbi/user-settings.mkfg</NCBI_SETTINGS>
<OS>linux</OS>
<PWD>/mnt</PWD>
<USER>ubuntu</USER>
<VDB_CONFIG/>
<VDB_ROOT/>
<config>
<default>true</default>
</config>
<kfg>
<arch>
<bits>64</bits>
<name>practice2</name>
</arch>
<dir>/home/ubuntu/.ncbi</dir>
<name>user-settings.mkfg</name>
</kfg>
<repository>
<remote>
<main>
<CGI>
<resolver-cgi>https://www.ncbi.nlm.nih.gov/Traces/names/names.fcgi</resolver-cgi>
</CGI>
</main>
<protected>
<CGI>
<resolver-cgi>https://www.ncbi.nlm.nih.gov/Traces/names/names.fcgi</resolver-cgi>
</CGI>
</protected>
</remote>
<user>
<main>
<public>
<apps>
<file>
<volumes>
<flat>files</flat>
</volumes>
</file>
<nakmer>
<volumes>
<nakmerFlat>nannot</nakmerFlat>
</volumes>
</nakmer>
<nannot>
<volumes>
<nannotFlat>nannot</nannotFlat>
</volumes>
</nannot>
<refseq>
<volumes>
<refseq>refseq</refseq>
</volumes>
</refseq>
<sra>
<volumes>
<sraFlat>sra</sraFlat>
</volumes>
</sra>
<wgs>
<volumes>
<wgsFlat>wgs</wgsFlat>
</volumes>
</wgs>
</apps>
<root>/home/ubuntu/ncbi/public</root>
</public>
</main>
</user>
</repository>
<tools>
<ascp>
<max_rate>450m</max_rate>
</ascp>
</tools>
<vdb>
<lib>
<paths>
<kfg>/mnt/miniconda2/bin</kfg>
</paths>
</lib>
</vdb>
</Config>
tle003
@tle003
Dec 17 2018 16:39
Is this error related to the installation of the Entrez direct tool?
Isaac Overcast
@isaacovercast
Dec 17 2018 17:29
@jonatanleo https://ipyrad.readthedocs.io/parameters.html#pop-assign-file
One or more additional lines should be included that start with one or more “#” characters. These special lines tell ipyrad how many samples must have data within each population for the locus to be retained in the final assembly, and thus assign different min_samples_locus values to each population. This will override the global min_samples_locus value.
@jonatanleo Just add a # at the beginning of the last line and you should be good to go.
Isaac Overcast
@isaacovercast
Dec 17 2018 18:45
@tle003 conda install -c bioconda perl-lwp-protocol-https
Not sure why this didn't install with the entrez tools originally.
tle003
@tle003
Dec 17 2018 19:34
Hi - I did as instructed and it updated my conda installation. I then ran the code again and got the same error as we discussed before. I also tried to update Entrez-direct and sra-tools, but there were no changes made to those installations.
Isaac Overcast
@isaacovercast
Dec 17 2018 20:53
Did you try running the esearch command again to test if my suggested fix worked? I just pulled that out by searching anaconda, it might not have actually fixed the problem.
tle003
@tle003
Dec 17 2018 21:43
I tried the esearch command again and got the same error. Would this be related to my security group ingress settings with the cloud server that I am working with?
Isaac Overcast
@isaacovercast
Dec 17 2018 22:53
Could be. It's clear that the salient error info is: "Protocol scheme 'https' is not supported (LWP::Protocol::https not installed)", so it looks like for some reason the perl https module is still not getting seen. Maybe its something with your perl path? It's an environment issue certainly.