Question: evigene pipeline failure: missing cdna_bestorf.pl
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gravatar for lplough
3.6 years ago by
lplough30
lplough30 wrote:

Hi
I am trying out the evigene evidential gene pipeline http://arthropods.eugenes.org/EvidentialGene/ on some multi K-mer transcriptome assemblies.

I have had a difficult time getting it to run even on simple data or to debug. It seems to fail to find various perl scripts that are sub components of the main pipeline, tr2aacds.pl, that should be in the PATH or in directories that I thought it would find. So, I must be misunderstanding how to set up the pipeline. There is relatively little documentation, and I don't need to run it on a cluster. I am just trying to run it locally.

So, the latest warning I get is an error finding the cdna_bestorf.pl script, a major sub component:

.../evigene/scripts/prot# env trset=Bridger_ALL.fasta.gz datad=`pwd` ./tr2aacds_test2.sh  
/usr/bin//evigene/prot/tr2aacds.pl -tidy -NCPU 2 -MAXMEM 1000 -log -cdna Bridger_ALL.fasta.gz
#t2ac: FATAL evigeneapp=cdna_bestorf.pl, path=echo MISSING_cdna_bestorf.pl

The returned second line is the call to the main pipeline script, and the third line is the error.

The missing script cdna_bestorf.pl) is in the same directory ('scripts/prot') I am running tr2aacds_test2.sh from, which basically calls the main script tr2aacds.pl. I also put the cdna_bestorf in the global path, so can be called from anywhere.

Perhaps it is more informative if I run it directly and debug;

/usr/bin/evigene# ./prot/tr2aacds.pl -mrna Bridger_ALL.fasta.gz -debug

#t2ac: EvidentialGene tr2aacds.pl VERSION 2013.07.27
#t2ac: app=blastn, path=/usr/bin/blastn
#t2ac: app=makeblastdb, path=/usr/bin/makeblastdb
#t2ac: app=lastz, path=echo MISSING_lastz
#t2ac: app=fastanrdb, path=/usr/bin/fastanrdb
#t2ac: app=cd-hit-est, path=/usr/bin/cd-hit-est
#t2ac: app=cd-hit, path=/usr/bin/cd-hit
#t2ac: evigeneapp=cdna_bestorf.pl, path=echo MISSING_cdna_bestorf.pl
#t2ac: evigeneapp=prot/traa2cds.pl, path=echo MISSING_prot/traa2cds.pl
#t2ac: evigeneapp=rnaseq/asmrna_dupfilter2.pl, path=echo MISSING_rnaseq/asmrna_dupfilter2.pl
#t2ac: evigeneapp=prot/aaqual.sh, path=echo MISSING_prot/aaqual.sh
#t2ac: BEGIN with cdnaseq= Bridger_ALL.fasta.gz date= Sun Nov  6 15:52:03 EST 2016
#t2ac: CMD= echo MISSING_cdna_bestorf.pl -nostop -minaa=30 -cdna Bridger_ALL.fasta.gz -aaseq Bridger_ALL.aa -cdsseq Bridger_ALL.cds
MISSING_cdna_bestorf.pl -nostop -minaa=30 -cdna Bridger_ALL.fasta.gz -aaseq Bridger_ALL.aa -cdsseq Bridger_ALL.cds
#t2ac: bestorf_cds= Bridger_ALL.cds nrec= 0
#t2ac: CMD= echo MISSING_prot/aaqual.sh Bridger_ALL.aa
MISSING_prot/aaqual.sh Bridger_ALL.aa
#t2ac: CMD= /usr/bin/fastanrdb Bridger_ALL.cds > Bridger_ALLnr.cds
** FATAL ERROR **: Cannot read file [Bridger_ALL.cds]
exiting ...
#t2ac: ERR=256  /usr/bin/fastanrdb Bridger_ALL.cds > Bridger_ALLnr.cds
#t2ac: nonredundant_cds= Bridger_ALLnr.cds nrec= 0
#t2ac: ERR: nonredundant_reassignbest missing cdsnr:Bridger_ALLnr.cds or aaqual:Bridger_ALL.aa.qual
#t2ac: nonredundant_reassignbest= 0 of 0
#t2ac: CMD= /usr/bin/cd-hit-est  -c 1.00 -M 1000 -l 89 -d 0 -i Bridger_ALLnr.cds -o Bridger_ALLnrcd1.cds 1> Bridger_ALLnrcd1.log 2>&1
#t2ac: nofragments_cds= Bridger_ALLnrcd1.cds nrec= 0
#t2ac: blastn_cds= Bridger_ALLnrcd1-self98.blastn
#t2ac: CMD= echo MISSING_rnaseq/asmrna_dupfilter2.pl -debug -tinyaln 35 -aasize Bridger_ALL.aa.qual -CDSALIGN -blastab Bridger_ALLnrcd1-self98.blastn   -outeqtab Bridger_ALL.alntab -outclass Bridger_ALL.trclass >Bridger_ALL.adupfilt.log 2>&1
#t2ac: asmdupfilter_cds= Bridger_ALL.trclass
#t2ac: ERR: asmdupclass_sum missing: Bridger_ALL.trclass
#t2ac: ERR: asmdupclass_fileset missing: Bridger_ALL.trclass
#t2ac: asmdupfilter_fileset= -1
#t2ac: DONE at date= Sun Nov  6 15:52:03 EST 2016
#t2ac: ======================================

The aaqual.pl script is also mssing.

I suspect I need to alter the path to the 'evigeneapp' so it points to the right directories, but, im not sure how to do that directly.

Any help would be much appreciated.

Thanks.

transcriptome rna-seq evigene • 1.4k views
ADD COMMENTlink modified 8 weeks ago by tomeksilentfall0 • written 3.6 years ago by lplough30
0
gravatar for tomeksilentfall
8 weeks ago by
tomeksilentfall0 wrote:

Hello,

I come to this problem just today and I realize that these missing parts like MISSING_cdna_bestorf.pl have no rights. So chmod +x ../cdna_bestorf.pl should do the trick. I know its really old question but maybe somebody will also strugle with that.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by tomeksilentfall0
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