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
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.
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.
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: 5a26a6e85dTransPi - 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
[- ] 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.runI don't understand the error. I do not know how to fix it. Help me, please.
Thank you so much! Scarleth