tr2aacds error about class2pub

Question

[380630938]

Hey,

This may be real simple, but I'm having issues with running tr2aacds.pl to get non-redundant transcripts. I have never had a problem like this with any other script. Any ideas?

The command:

tr2aacds.pl -tidy -NCPU 10  -logfile tr2aacds.log -cdna total.longest.fa

Use of uninitialized value $okaa in -f at /data/jiao/biosoft/evigene/scripts/genes/../cdna_evigenesub.pm line 811.
Use of uninitialized value $altaa in -f at /data/jiao/biosoft/evigene/scripts/genes/../cdna_evigenesub.pm line 812.
#readPubidTab(publicset/total.longest.pubids)= 83683
# nin=220382, nok=122061, nfrag=271, nskipnotloc=92571, nskipdupfrag=966, nskipdiffloc=4513
#insertUniqExons= 533
#collectExonChains= 83209 of 83416 ids
#assignChainLoci
#n_class: ichain=67308 icalt=12786 icsub=3115 icdup=207
#n_alts : t1=67308 t2=7927 t3=2853 t4=1260 t5=510 t6=164 t7=45 t8=12 t9=6 t10=2 t11=2 t12=2 t13=2 t14=1 t15=0 t16=0 t17=0 t18=0 t19=0 t20=0
Use of uninitialized value $okaa in -f at /data/jiao/biosoft/evigene/scripts/genes/../cdna_evigenesub.pm line 811.
Use of uninitialized value $altaa in -f at /data/jiao/biosoft/evigene/scripts/genes/../cdna_evigenesub.pm line 812.
#egr: FATAL Missing mrna

and, total.longest.class2pub.log has some error:

#egr: /data/jiao/biosoft/evigene/scripts/prot/../genes/trclass2pubset.pl  -noaltdrops -exontab tmpfiles/total.longestnrcd1x.exontab -log -debug -class total.longest.trclass
#egr: BEGIN /data/jiao/biosoft/evigene/scripts/prot/../genes/trclass2pubset.pl  input= total.longest date= 20220518
#egr: Make mRNA publicset/total.longest.mrna from okayset transcripts
#egr: evigeneapp=prot/traa2cds.pl, path=/data/jiao/biosoft/evigene/scripts/genes/../prot/traa2cds.pl
#egr: ERR: openRead publicset/total.longest.mrna
#egr: make mRNA publicset/total.longest.mrna: missing files oktr=./okayset/total.longest.okay.tr,okaa=missing,alttr=./okayset/total.longest.okalt.tr,altaa=missing,
        from (oktr,alttr)=getOkFileset(path=./okayset,suffix=tr|cdna|fasta|fna)
#egr: get_evgtrset=  . total.longest
#egr: FATAL Missing mrna

Thanks!

Answer 1

[Cathia]

Hi

Did you find where was the problem ?

I have the same error today, but a week ago, it was working...