Request re

We develop MH Guide, a genome-guided cancer treatment decision support software (

I was trying to get the current annotated pseudogene information via The link to GENCODE seems not to work and returns “file not found” (

Could you please kindly redirect me to the file with annotated pseudogenes.

If you are looking for the current GENCODE annotation, for the current release please follow this link: . If you want to use pseudo pipe to create a custom human annotation of a genome sequence of preferences, please follow the instructions here: . If you are interested in the functional annotation of pseudogenes with information regarding pseudogene activity please see .

Trying to execute Pseudopipe but I am running into multiple errors

I am trying to execute Pseudopipe but I am running into multiple errors. I have downloaded the latest version from the website and the command I am using to run it is

/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/ /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chrI_exLocs 0

I keep getting the following errors:

Making directories
Copying sequences
Fomatting the DNAs
/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/ line 84: /home/bp272/bin/blast-2.2.13/bin/formatdb: No such file or directory
Preparing the blast jobs
Skipping blast
Processing blast output
/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/ line 114: /home/bp272/bin/Python-2.6.6/python: No such file or directory
Finished processing blast output
Running Pseudopipe on both strands
Working on M strand
/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/ line 144: /home/bp272/bin/Python-2.6.6/python: No such file or directory
Finished Pseudopipe on strand M
Working on P strand
/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/pseudopipe/bin/ line 144: /home/bp272/bin/Python-2.6.6/python: No such file or directory
Finished Pseudopipe on strand P
Generating final results
find: ‘/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/minus/pgenes’: No such file or directory
find: ‘/work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/plus/pgenes’: No such file or directory
gzip: /work/LAS/rpwise-lab/sagnik/finder/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/*/pgenes/*.all.fa: No such file or directory
Finished generating pgene full alignment
Finished running Pseudopipe

I am running this inside conda environment. I tried executing it outside but it gave me the same errors. Could you please help?

I have posted on the website under the comments section by mistake. Please excuse my ignorance.

It seems that you did not set the environment file ( correctly. You may need to set the it as the following and put in the same dir as &

if [ ! -z "$PSEUDOPIPE_ENV" ]; then source $PSEUDOPIPE_ENV; return; fi

# Pseudopipe configuration

export PSEUDOPIPE_HOME=`cd \`dirname $0\`/../; pwd`

export pseudopipe=$PSEUDOPIPE_HOME/core/

export genPgeneResult=$PSEUDOPIPE_HOME/ext/

export genFullAln=$PSEUDOPIPE_HOME/ext/

export fastaSplitter=$PSEUDOPIPE_HOME/ext/

export sqDedicated=$PSEUDOPIPE_HOME/ext/

export sqDummy=$PSEUDOPIPE_HOME/ext/

export blastHandler=$PSEUDOPIPE_HOME/core/

export extractExLoc=$PSEUDOPIPE_HOME/core/ #

# Python configuration

export pythonExec=/bin/python2

# Alignment tools configuration

export formatDB=/ysm-gpfs/pi/gerstein/yy532/software/blast-2.2.13/bin/formatdb

export blastExec=/ysm-gpfs/pi/gerstein/yy532/software/blast-2.2.13/bin/blastall

export fastaExec=/ysm-gpfs/pi/gerstein/yy532/software/fasta-35.1.5/tfasty35

Thank you for your reply. I am using python3 in my pipeline. Will this code work for python3?

Please use python2.