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naturalis / bio-cipres

Phylogenomic analysis on the CIPRES REST portal
MIT License
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Documentation #10

Open ambarishK opened 4 years ago

ambarishK commented 4 years ago

Please specify more to add onto Documentation.md

ambarishK commented 4 years ago

MAFFT runs fine.

ngsap2@ubuntu:~/bio-cipres$ cipresrun -t MAFFT_XSEDE -p vparam.anysymbol_=1 -i /home/ngsap2/bio-cipres/data/unalign.fasta -y cipres_appinfo.yml -o output.mafft=/home/ngsap2/bio-cipres/outfile.fastaINFO Bio::Phylo::CIPRES::yml [Bio/Phylo/CIPRES.pm 241] - Reading YAML file cipres_appinfo.yml
INFO Bio::Phylo::CIPRES::launch_job [Bio/Phylo/CIPRES.pm 145] - Job launched at https://cipresrest.sdsc.edu/cipresrest/v1/job/ambarish/NGBW-JOB-MAFFT_XSEDE-9B749403AB7142DC8008D18E790C0440
INFO Bio::Phylo::CIPRES::check_status [Bio/Phylo/CIPRES.pm 162] - Going to check status for https://cipresrest.sdsc.edu/cipresrest/v1/job/ambarish/NGBW-JOB-MAFFT_XSEDE-9B749403AB7142DC8008D18E790C0440
INFO Bio::Phylo::CIPRES::check_status [Bio/Phylo/CIPRES.pm 179] - [Fri Apr 24 04:27:45 2020] completed: false
INFO Bio::Phylo::CIPRES::check_status [Bio/Phylo/CIPRES.pm 162] - Going to check status for https://cipresrest.sdsc.edu/cipresrest/v1/job/ambarish/NGBW-JOB-MAFFT_XSEDE-9B749403AB7142DC8008D18E790C0440
INFO Bio::Phylo::CIPRES::check_status [Bio/Phylo/CIPRES.pm 179] - [Fri Apr 24 04:28:48 2020] completed: true
INFO Bio::Phylo::CIPRES::clean_job [Bio/Phylo/CIPRES.pm 325] - Going to clean job https://cipresrest.sdsc.edu/cipresrest/v1/job/ambarish/NGBW-JOB-MAFFT_XSEDE-9B749403AB7142DC8008D18E790C0440

Error while running IQTREE

ngsap2@ubuntu:~/bio-cipres$ cipresrun -t IQTREE_XSEDE -p vparam.specify_runtype_=2 -p vparam.specify_dnamodel_=HKY -p vparam.bootstrap_type_=bb -p vparam.use_bnni_=1 -p vparam.num_bootreps_=1000 -p vparam.specify_numparts_=1 -i /home/ngsap2/bio-cipres/outfile.fasta -y cipres_appinfo.yml -o output.contree=/home/ngsap2/bio-cipres/tree.dnd
INFO Bio::Phylo::CIPRES::yml [Bio/Phylo/CIPRES.pm 241] - Reading YAML file cipres_appinfo.yml
INFO Bio::Phylo::CIPRES::launch_job [Bio/Phylo/CIPRES.pm 145] - Job launched at https://cipresrest.sdsc.edu/cipresrest/v1/job/ambarish/NGBW-JOB-IQTREE_XSEDE-12AF7F07DA8A4058B6F60C3A32DFDB9E
INFO Bio::Phylo::CIPRES::check_status [Bio/Phylo/CIPRES.pm 162] - Going to check status for https://cipresrest.sdsc.edu/cipresrest/v1/job/ambarish/NGBW-JOB-IQTREE_XSEDE-12AF7F07DA8A4058B6F60C3A32DFDB9E
INFO Bio::Phylo::CIPRES::check_status [Bio/Phylo/CIPRES.pm 179] - [Fri Apr 24 04:33:03 2020] completed: true
-------------------------- EXCEPTION ----------------------------
Message: 400 URL missing

An exception of type Bio::Phylo::Util::Exceptions::NetworkError
was thrown.

This kind of error happens when a network resource can not be accessed.

Refer to the Bio::Phylo::Util::Exceptions documentation for more
information.
------------------------- STACK TRACE ---------------------------
STACK: Bio::Phylo::CIPRES::get_results('Bio::Phylo::CIPRES=HASH(0x3089ec0)', 'https://cipresrest.sdsc.edu/cipresrest/v1/job/ambarish/NGBW-JOB-IQTREE_XSEDE-12AF7F07DA8A4058B6F60C3A32DFDB9E/output') called at /usr/local/share/perl/5.22.1/Bio/Phylo/CIPRES.pm line 114
STACK: Bio::Phylo::CIPRES::run('Bio::Phylo::CIPRES=HASH(0x3089ec0)') called at /usr/local/bin/cipresrun line 60 
-----------------------------------------------------------------

Please resolve the error.

ambarishK commented 4 years ago

Hello sir. I am writing abstract for ISMB 2020 - GALAXY implementation of neoantigen prediction. I will mention your name as author...