johnsolk
commented
7 years ago Fixed by running make again. Since /mnt/home/ljcohen/TransDecoder-2.0.1/util/bin was already in the PATH, something must have happened during TransDecoder install the first time.
cd TransDecoder-2.0.1/
make
This is a problem with cd-hit-est and Transdecoder, but I've never encountered this error before and dammit dependencies passes so thought I should report.
/mnt/home/ljcohen/TransDecoder-2.0.1/TransDecoder.Predict -t /mnt/home/ljcohen/dammit_results/MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta.dammit/MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta --retain_long_orfs 600######################################## TaskFailed - taskid:TransDecoder.Predict:MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta Command failed: '/mnt/home/ljcohen/TransDecoder-2.0.1/TransDecoder.Predict -t /mnt/home/ljcohen/dammit_results/MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta.dammit/MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta --retain_long_orfs 600' returned 1which: no cd-hit-est in (/mnt/home/ljcohen/TransDecoder-2.0.1/util/bin:/mnt/home/ljcohen/.conda/envs/dammit/bin:/opt/software/ged-software/parallel/bin:/opt/software/OpenMPI/1.6.5--GCC-4.8.2/bin:/opt/software/GCC/4.8.3/bin:/mnt/home/ljcohen/BUSCO_v1.1b1:/mnt/home/ljcohen/TransDecoder-2.0.1:/mnt/home/ljcohen/.gem/ruby/1.8/bin:/mnt/home/ljcohen/bin/ncbi-blast-2.3.0+/bin:/mnt/home/ljcohen/bin/linuxbrew/bin:/mnt/home/ljcohen/anaconda2/bin:/mnt/home/ljcohen/bin/linuxbrew/sbin:/opt/software/Stata/13.0:/opt/software/MATLAB/R2014a/bin:/opt/software/cmake/2.8.5--GCC-4.4.5/bin:/usr/lib64/qt-3.3/bin:/opt/software/lmod/bin:/opt/moab/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/hpcc/bin:/opt/ibutils/bin:/mnt/home/ljcohen/bin/sratoolkit.2.5.4-1-ubuntu64/bin:/mnt/home/ljcohen/bin/transrate-1.0.1-linux-x86_64:/mnt/home/ljcohen/bin:/mnt/home/ljcohen/bin/transrate-1.0.3-linux-x86_64:/mnt/home/ljcohen/bin/transrate-1.0.3-linux-x86_64/bin:/mnt/home/ljcohen/bin/OrthoFinder-master:/mnt/home/ljcohen/bin/ncbi-blast-2.4.0+/bin:/mnt/home/ljcohen/bin/mcl/bin:/home/ubuntu/sratoolkit.2.5.4-1-ubuntu64/bin) Error, path to a required program (cd-hit-est) cannot be found
(dammit)[ljcohen@dev-intel14 dammit_results]$ dammit dependencies
dammit
a tool for easy de novo transcriptome annotation
by Camille Scott
v1.0.dev0, 2016
submodule: dependencies
All dependencies fulfilled.