problems running full analysis (--all option) and evigene's script

[BravoScarleth]

Hi Ramón,

I'm running the --all module and I get an error just when I should be using an evigene script. For some reason I don't know, the file combined.okay.fa is not created. All the others are created, but not that one.
This is the output I got.

nextflow run TransPi.nf --all --reads '/run/media/DataProcessing/tiburon/teste/R[1,2].fq.gz' --k 25,41,53,61 --maxReadLen 100 --outdir /run/media/DataProcessing/tiburon/teste/ -profile conda
N E X T F L O W ~ version 21.04.1
Launching TransPi.nf [admiring_woese] - revision: 5a26a6e85d

TransPi - Transcriptome Analysis Pipeline v1.3.0-rc

TransPi.nf Directory: /home/sbravo/Descargas/TransPi/TransPi.nf
Launch Directory: /home/sbravo/Descargas/TransPi
Results Directory: /run/media/DataProcessing/tiburon/teste/
Work Directory: /home/sbravo/Descargas/TransPi/work
TransPi DBs: /home/sbravo/Descargas/TransPi
Uniprot DB: /run/media/DataProcessing/DBs/uniprot_db/uniprot_metazoa_33208.fasta
Busco DB: /run/media/DataProcessing/DBs/busco_db/metazoa_odb10/
Reads Directory: /run/media/DataProcessing/tiburon/teste/R[1,2].fq.gz
Read Length: 100
Kmers: 25,41,53,61

Running TransPi with your dataset


Running the full TransPi analysis

[- ] process > fasqc -
[- ] process > fastp -
[- ] process > fasqc -
[- ] process > fastp -
[- ] process > fastp_stats -
[- ] process > skip_rrna_removal -
[- ] process > normalize_reads -
[- ] process > trinity_assembly -
[- ] process > soap_assembly -
executor > local (1)
...

executor > local (14)
[a1/b551cf] process > fasqc (R) [100%] 1 of 1 ✔
[a1/db5052] process > fastp (R) [100%] 1 of 1 ✔
[08/2cd9ee] process > fastp_stats (R) [100%] 1 of 1 ✔
[44/4a8458] process > skip_rrna_removal (R) [100%] 1 of 1 ✔
[d3/7e1697] process > normalize_reads (R) [100%] 1 of 1 ✔
[f6/ec9860] process > trinity_assembly (R) [100%] 1 of 1 ✔
[26/0bdb02] process > soap_assembly (R) [100%] 1 of 1 ✔
[d6/b4833e] process > velvet_oases_assembly (R) [100%] 1 of 1 ✔
[6a/86e1f1] process > rna_spades_assembly (R) [100%] 1 of 1 ✔
[09/779b72] process > transabyss_assembly (R) [100%] 1 of 1 ✔
[d2/04067d] process > evigene (R) [ 0%] 0 of 1
[- ] process > rna_quast -
[- ] process > mapping_evigene -
[- ] process > busco4 -
[d7/40bafd] process > mapping_trinity (R) [100%] 1 of 1 ✔
[- ] process > summary_evigene_individual -
[- ] process > busco4_tri -
[b3/bf26e0] process > skip_busco_dist (R) [100%] 1 of 1 ✔
[- ] process > summary_busco4_individual -
[- ] process > get_busco4_comparison -
[- ] process > transdecoder_longorf -
[- ] process > transdecoder_diamond -
[- ] process > transdecoder_hmmer -
[- ] process > transdecoder_predict -
[- ] process > swiss_diamond_trinotate -
[- ] process > custom_diamond_trinotate -
[- ] process > hmmer_trinotate -
[- ] process > skip_signalP -
[- ] process > skip_tmhmm -
[- ] process > skip_rnammer -
[- ] process > trinotate -
[- ] process > get_GO_comparison -
[- ] process > summary_custom_uniprot -
[- ] process > skip_kegg -
[- ] process > get_transcript_dist -
[- ] process > summary_transdecoder_individual -
[- ] process > summary_trinotate_individual -
[- ] process > get_report -
[c3/fa967a] process > get_run_info [100%] 1 of 1 ✔
Error executing process > 'evigene (R)'

Caused by:
Process evigene (R) terminated with an error exit status (1)

Command executed:

echo -e "\n-- Starting EviGene --\n"

cat R.Velvet.fa R.SOAP.fa R.SPADES.fa R.Trinity.fa R.TransABySS.fa >R.combined.fa

/home/sbravo/Descargas/TransPi/scripts/evigene/scripts/prot/tr2aacds.pl -tidy -NCPU 15 -MAXMEM 153600 -log -cdna R.combined.fa

echo -e "\n-- DONE with EviGene --\n"

cp okayset/combined.okay.fa R.combined.okay.fa
cp okayset/combined.okay.cds R.combined.okay.cds

if [ -d tmpfiles/ ];then
rm -rf tmpfiles/
fi

v=$( echo "2019.05.14" )
echo "EvidentialGene: $v" >evigene.version.txt
v=$( blastn -version | head -n1 | awk '{print $2}' )
echo "Blast: $v" >>evigene.version.txt
v=$( cd-hit -h | head -n1 | cut -f 1 -d "(" | cut -f 2 -d "n" )
echo "CD-HIT: $v" >>evigene.version.txt
v=$( exonerate -v | head -n1 | cut -f 5 -d " " )
echo "Exonerate: $v" >>evigene.version.txt

Command exit status:
1

Command output:

-- Starting EviGene --

-- DONE with EviGene --

Command error:
Use of uninitialized value $okaa in -f at /home/sbravo/Descargas/evigene/scripts/genes/../cdnexecutor > local (14)
[a1/b551cf] process > fasqc (R) [100%] 1 of 1 ✔
[a1/db5052] process > fastp (R) [100%] 1 of 1 ✔
[08/2cd9ee] process > fastp_stats (R) [100%] 1 of 1 ✔
[44/4a8458] process > skip_rrna_removal (R) [100%] 1 of 1 ✔
[d3/7e1697] process > normalize_reads (R) [100%] 1 of 1 ✔
[f6/ec9860] process > trinity_assembly (R) [100%] 1 of 1 ✔
[26/0bdb02] process > soap_assembly (R) [100%] 1 of 1 ✔
[d6/b4833e] process > velvet_oases_assembly (R) [100%] 1 of 1 ✔
[6a/86e1f1] process > rna_spades_assembly (R) [100%] 1 of 1 ✔
[09/779b72] process > transabyss_assembly (R) [100%] 1 of 1 ✔
[d2/04067d] process > evigene (R) [100%] 1 of 1, failed: 1 ✘
[- ] process > rna_quast -
[- ] process > mapping_evigene -
[- ] process > busco4 -
[d7/40bafd] process > mapping_trinity (R) [100%] 1 of 1 ✔
[- ] process > summary_evigene_individual -
[- ] process > busco4_tri -
[b3/bf26e0] process > skip_busco_dist (R) [100%] 1 of 1 ✔
[- ] process > summary_busco4_individual -
[- ] process > get_busco4_comparison -
[- ] process > transdecoder_longorf -
[- ] process > transdecoder_diamond -
[- ] process > transdecoder_hmmer -
[- ] process > transdecoder_predict -
[- ] process > swiss_diamond_trinotate -
[- ] process > custom_diamond_trinotate -
[- ] process > hmmer_trinotate -
[- ] process > skip_signalP -
[- ] process > skip_tmhmm -
[- ] process > skip_rnammer -
[- ] process > trinotate -
[- ] process > get_GO_comparison -
[- ] process > summary_custom_uniprot -
[- ] process > skip_kegg -
[- ] process > get_transcript_dist -
[- ] process > summary_transdecoder_individual -
[- ] process > summary_trinotate_individual -
[- ] process > get_report -
[c3/fa967a] process > get_run_info [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit

Something went wrong. Check error message below and/or log files.
Error executing process > 'evigene (R)'

Caused by:
Process evigene (R) terminated with an error exit status (1)

Command executed:

echo -e "\n-- Starting EviGene --\n"

cat R.Velvet.fa R.SOAP.fa R.SPADES.fa R.Trinity.fa R.TransABySS.fa >R.combined.fa

/home/sbravo/Descargas/TransPi/scripts/evigene/scripts/prot/tr2aacds.pl -tidy -NCPU 15 -MAXMEM 153600 -log -cdna R.combined.fa

echo -e "\n-- DONE with EviGene --\n"

cp okayset/combined.okay.fa R.combined.okay.fa
cp okayset/combined.okay.cds R.combined.okay.cds

if [ -d tmpfiles/ ];then
rm -rf tmpfiles/
fi

v=$( echo "2019.05.14" )
echo "EvidentialGene: $v" >evigene.version.txt
v=$( blastn -version | head -n1 | awk '{print $2}' )
echo "Blast: $v" >>evigene.version.txt
v=$( cd-hit -h | head -n1 | cut -f 1 -d "(" | cut -f 2 -d "n" )
echo "CD-HIT: $v" >>evigene.version.txt
v=$( exonerate -v | head -n1 | cut -f 5 -d " " )
echo "Exonerate: $v" >>evigene.version.txt

Command exit status:
1

Command output:

-- Starting EviGene --

-- DONE with EviGene --

Command error:
Use of uninitialized value $okaa in -f at /home/sbravo/Descargas/evigene/scripts/genes/../cdnexecutor > local (14)
[a1/b551cf] process > fasqc (R) [100%] 1 of 1 ✔
[a1/db5052] process > fastp (R) [100%] 1 of 1 ✔
[08/2cd9ee] process > fastp_stats (R) [100%] 1 of 1 ✔
[44/4a8458] process > skip_rrna_removal (R) [100%] 1 of 1 ✔
[d3/7e1697] process > normalize_reads (R) [100%] 1 of 1 ✔
[f6/ec9860] process > trinity_assembly (R) [100%] 1 of 1 ✔
[26/0bdb02] process > soap_assembly (R) [100%] 1 of 1 ✔
[d6/b4833e] process > velvet_oases_assembly (R) [100%] 1 of 1 ✔
[6a/86e1f1] process > rna_spades_assembly (R) [100%] 1 of 1 ✔
[09/779b72] process > transabyss_assembly (R) [100%] 1 of 1 ✔
[d2/04067d] process > evigene (R) [100%] 1 of 1, failed: 1 ✘
[- ] process > rna_quast -
[- ] process > mapping_evigene -
[- ] process > busco4 -
[d7/40bafd] process > mapping_trinity (R) [100%] 1 of 1 ✔
[- ] process > summary_evigene_individual -
[- ] process > busco4_tri -
[b3/bf26e0] process > skip_busco_dist (R) [100%] 1 of 1 ✔
[- ] process > summary_busco4_individual -
[- ] process > get_busco4_comparison -
[- ] process > transdecoder_longorf -
[- ] process > transdecoder_diamond -
[- ] process > transdecoder_hmmer -
[- ] process > transdecoder_predict -
[- ] process > swiss_diamond_trinotate -
[- ] process > custom_diamond_trinotate -
[- ] process > hmmer_trinotate -
[- ] process > skip_signalP -
[- ] process > skip_tmhmm -
[- ] process > skip_rnammer -
[- ] process > trinotate -
[- ] process > get_GO_comparison -
[- ] process > summary_custom_uniprot -
[- ] process > skip_kegg -
[- ] process > get_transcript_dist -
[- ] process > summary_transdecoder_individual -
[- ] process > summary_trinotate_individual -
[- ] process > get_report -
[c3/fa967a] process > get_run_info [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit

Something went wrong. Check error message below and/or log files.
Error executing process > 'evigene (R)'

Caused by:
Process evigene (R) terminated with an error exit status (1)

Command executed:

echo -e "\n-- Starting EviGene --\n"

cat R.Velvet.fa R.SOAP.fa R.SPADES.fa R.Trinity.fa R.TransABySS.fa >R.combined.fa

/home/sbravo/Descargas/TransPi/scripts/evigene/scripts/prot/tr2aacds.pl -tidy -NCPU 15 -MAXMEM 153600 -log -cdna R.combined.fa

echo -e "\n-- DONE with EviGene --\n"

cp okayset/combined.okay.fa R.combined.okay.fa
cp okayset/combined.okay.cds R.combined.okay.cds

if [ -d tmpfiles/ ];then
rm -rf tmpfiles/
fi

v=$( echo "2019.05.14" )
echo "EvidentialGene: $v" >evigene.version.txt
v=$( blastn -version | head -n1 | awk '{print $2}' )
echo "Blast: $v" >>evigene.version.txt
v=$( cd-hit -h | head -n1 | cut -f 1 -d "(" | cut -f 2 -d "n" )
echo "CD-HIT: $v" >>evigene.version.txt
v=$( exonerate -v | head -n1 | cut -f 5 -d " " )
echo "Exonerate: $v" >>evigene.version.txt

Command exit status:
1

Command output:

-- Starting EviGene --

-- DONE with EviGene --

Command error:
Use of uninitialized value $okaa in -f at /home/sbravo/Descargas/evigene/scripts/genes/../cdna_evigenesub.pm line 814.
Use of uninitialized value $altaa in -f at /home/sbravo/Descargas/evigene/scripts/genes/../cdna_evigenesub.pm line 815.
#readPubidTab(publicset/R.combined.pubids)= 8394

nin=63492, nok=16561, nfrag=168, nskipnotloc=45359, nskipdupfrag=1121, nskipdiffloc=283

#insertUniqExons= 167
#collectExonChains= 8166 of 8237 ids
#assignChainLoci
#n_class: ichain=5796 icalt=1144 icsub=1226 icdup=71
#n_alts : t1=5796 t2=550 t3=202 t4=103 t5=65 t6=46 t7=31 t8=21 t9=17 t10=15 t11=12 t12=8 t13=8 t14=6 t15=5 t16=5 t17=5 t18=4 t19=4 t20=3
Use of uninitialized value $okaa in -f at /home/sbravo/Descargas/evigene/scripts/genes/../cdna_evigenesub.pm line 814.
Use of uninitialized value $altaa in -f at /home/sbravo/Descargas/evigene/scripts/genes/../cdna_evigenesub.pm line 815.
#egr: FATAL Missing mrna
cp: no se puede efectuar `stat' sobre 'okayset/combined.okay.fa': No existe el fichero o el directorio

Work dir:
/home/sbravo/Descargas/TransPi/work/d2/04067d1da59bc7532be8e0e9217e1a

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

I don't understand the error. I do not know how to fix it.
Help me, please.

Thank you so much!
Scarleth