desmodus1984

I can't update conda because I am in a cluster, and I can't do that..

Hi Carlos, I did as suggested and I got the following outputs: which emapper.py~/.conda/envs/eggnob/bin/emapper.py which download_eggnog_database.py/usr/bin/which: no download_eggnog_database.py in (/users/PHS0338/jpac1984/.conda/envs/eggnob/bin:/usr/local/xalt/xalt/bin:/usr/local/python/3.6-conda5.2/bin:/users/PHS0338/jpac1984/.linuxbrew/bin:/users/PHS0338/jpac1984/.linuxbrew/sbin:/users/PHS0338/jpac1984/.cargo/bin:/users/PHS0338/jpac1984/perl5/bin:/opt/mvapich2/intel/19.0/2.3.3/bin:/usr/local/gnu/8.4.0/bin:/opt/intel/itac/2019.5.041/bin:/opt/intel/advisor_2019/bin64:/opt/intel/vtune_amplifier_2019/bin64:/opt/intel/inspector_2019/bin64:/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/usr/local/software_usage:/usr/lib64/qt-3.3/bin:/opt/osc/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/opt/ddn/ime/bin:/opt/puppetlabs/bin:/users/PHS0338/jpac1984/edirect) Hope that provide a suggestion of a potential solution. Thanks;...

Hi @qiyubio , Does that container come with Augustus? I am trying to install Augustus and I have a fatal error ../include/randseqaccess.hh:21:10: fatal error: mysql++/mysql++.h: No such file or directory...

Ok. Then, would it be okay to request a node with 150 GB and set the B parameter to 140 GB? Thanks;

Also, I wanted to try to parameterize a run using the paired de Bruijn graph mode. I sent my sample for sequencing and I got the following QC info for...

Hi, Please let me ask you another question. How much coverage does one need for error correction? I will do whole-genome resequencing, and to reduce variant call error I thought...

Hi, Wow, I expected a different result from the largest ~60X dataset. Have you heard about Athena? https://www.nature.com/articles/s41598-019-52196-4#Sec16 [https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fs41598-019-52196-4/MediaObjects/41598_2019_52196_Fig1_HTML.png] Athena: Automated Tuning of k-mer based Genomic Error Correction Algorithms using...

Thanks for the information. The small dataset test is finished with K-mer size of 65, and I got the following report: [2021-02-20 18:17:52] =============Start====================[2021-02-20 18:17:52] Scanning the input files to...

Dear Pierre, Thank you very much for your reply. I think that I managed to properly install it. I did get the 2nd error but with the correct command, I...

Hi Pierre, I think that I did something wrong. I did as you said, used the command: export PATH=$PWD/minimap2:/fs/scratch/PHS0338/appz/minimap2:$PATH and then ./install.sh. I am using the --minimapIndex 5G and I...