tr2aacds error about class2pub
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4 weeks ago
380630938 • 0

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!

tr2aacds class2pub error • 86 views
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