Error: FATAL Missing mrna

[Sai Reddy Achakkagari]

Hi,

I was trying to merge two different transcriptome assemblies using tr2aacds pipeline and encountered the following error. 

 #egr: FATAL Missing mrna

I was running tr2aacds.pl VERSION 2022.01.20 with the command...

tr2aacds.pl  -debug -NCPU=15 -MAXMEM=50000 -logfile -cdnaseq trinity.dn+gg.fa

last few lines of the tr2aacds.log file 

#t2ac: CMD= /mnt2/software/evigene/scripts/prot/../genes/trclass2pubset.pl -onlypub -norealt -noaltdrops -log -debug -class trinity.dn+gg.trclass

#t2ac: CMD= sort -k7,7nr -k2,2 -k6,6nr -k1,1 tmpfiles/trinity.dn+ggnrsmcd1x-self100.btall | env pubids=publicset/trinity.dn+gg.pubids debug=1 /mnt2/software/evigene/scripts/prot/../genes/blasttrset2exons2.pl > tmpfiles/trinity.dn+ggnrsmcd1x.exontab

#t2ac: CMD= /mnt2/software/evigene/scripts/prot/../genes/trclass2pubset.pl -noaltdrops -exontab tmpfiles/trinity.dn+ggnrsmcd1x.exontab  -log -debug  -class trinity.dn+gg.trclass

#t2ac: ERR=512  /mnt2/software/evigene/scripts/prot/../genes/trclass2pubset.pl -noaltdrops -exontab tmpfiles/trinity.dn+ggnrsmcd1x.exontab  -log -debug  -class trinity.dn+gg.trclass

#t2ac: DONE at date= Tue Dec  6 23:23:58 UTC 2022

#t2ac: ======================================

And the log file of trclass2pubset.pl looks like this..

#egr: EvidentialGene trclass2pubset VERSION 2020.03.15

#egr: /mnt2/software/evigene/scripts/prot/../genes/trclass2pubset.pl  -noaltdrops -exontab tmpfiles/trinity.dn+ggnrsmcd1x.exontab -log -debug -class trinity.dn+gg.trclass

#egr: BEGIN /mnt2/software/evigene/scripts/prot/../genes/trclass2pubset.pl  input= trinity.dn+gg date= 20221206

#egr: Make mRNA publicset/trinity.dn+gg.mrna from okayset transcripts

#egr: evigeneapp=prot/traa2cds.pl, path=/mnt2/software/evigene/scripts/genes/../prot/traa2cds.pl

#egr: ERR: openRead publicset/trinity.dn+gg.mrna

#egr: make mRNA publicset/trinity.dn+gg.mrna: missing files oktr=missing,okaa=missing,alttr=missing,altaa=missing,

        from (oktr,alttr)=getOkFileset(path=./okayset,suffix=tr|cdna|fasta|fna)

#egr: get_evgtrset=  . trinity.dn+gg

#egr: FATAL Missing mrna 

The directories have the following files.. 

okayset/
├── trinity.dn+gg.okalt.aa
├── trinity.dn+gg.okalt.cds
├── trinity.dn+gg.okalt.tr
├── trinity.dn+gg.okay.aa
├── trinity.dn+gg.okay.cds
└── trinity.dn+gg.okay.tr
dropset/
├── trinity.dn+gg.drop.aa
├── trinity.dn+gg.drop.cds
└── trinity.dn+gg.drop.tr
inputset/
├── trinity.dn+gg.aa
├── trinity.dn+gg.aa.qual
└── trinity.dn+gg.cds
tmpfiles/
├── trinity.dn+gg.adupfilt.log
├── trinity.dn+gg.alntab
├── trinity.dn+ggnr.cds
├── trinity.dn+ggnr.cds.isbest
├── trinity.dn+ggnr.cds.old
├── trinity.dn+ggnrsm.aa
├── trinity.dn+ggnrsm.cds
├── trinity.dn+ggnrsmcd1x-self100.btall
├── trinity.dn+ggnrsmcd1x-self98.blastn
├── trinity.dn+ggnrsmcd1x.cds
├── trinity.dn+ggnrsmcd1x.cds.qual
├── trinity.dn+ggnrsmcd1x.exontab
├── trinity.dn+ggnrsmcd1x_db.log
├── trinity.dn+ggnrxu.cds
├── trinity.dn+ggnrxucd1.cds
├── trinity.dn+ggnrxucd1.cds.clstr
├── trinity.dn+ggnrxucd1.cds.isbest
├── trinity.dn+ggnrxucd1.cds.old
└── trinity.dn+ggnrxucd1.log
publicset/
├── trinity.dn+gg.mainalt.tab
├── trinity.dn+gg.pubids
├── trinity.dn+gg.pubids.old
└── trinity.dn+gg.pubids.realt.log

Could you please help me understand what the issue here is. 

Thank you for your time! 

Sai

[Aaqib Javid]

Hi Sai, 

  I dont know much about evigene, but Im trying to learn. 

As far as I know, first you have to change the extension of the 1.fasta 2.fasta 3.fasta > all.fasta.tr[.gz]

you can find this pipeline in /evigene/scripts/rnaseq/trformat.pl 

Hope it may help you ! 

[Sai Reddy Achakkagari]

Hey, 

Thanks! It was resolved after Don suggested me to change the file name, the special characters are making it not work.
Sai