No reference genomes were configured, please adjust configuration

[Linnaeus001]

Hi there, I got a problem about fastq-screen and wish to have your help :) let me show you my process (my aim is to map my data onto some specific species)

Since i build up a new empty /.conf file for the configuration: $ touch 1.conf I edit the content inside of it with emacs (through xmanager7) and got:

$ less 1.conf BWA /home/DataDisk/th_data/software/envs/bwa THREADS 8 DATABASE x.ph /home/DataDisk/th_data/workplace/de-contamination/database_custom/x.phaseoli DATABASE s.mp /home/Datadisk/th_data/workplace/de-contamination/database_custom/s.marcescens_plas DATABASE s.mc /home/Datadisk/th_data/workplace/de-contamination/database_custom/s.marcescens_chr DATABASE p.to /home/Datadisk/th_data/workplace/de-contamination/database_custom/p.tolaasii DATABASE homo /home/Datadisk/th_data/workplace/de-contamination/database_custom/hg19 DATABASE s.gr /home/Datadisk/th_data/workplace/de-contamination/database_custom/GCF_023897955.1_iqSchGreg1.2_genomic DATABASE e.coli /home/Datadisk/th_data/workplace/de-contamination/database_custom/e.coli

And make index of it: $ bwa index [each .fa files] $ ls 1.conf hg19.fa s.marcescens_chr.fasta.pac 1.conf~ hg19.fa.amb s.marcescens_chr.fasta.sa 89-1112_1.fq.gz hg19.fa.ann s.marcescens_plas.fasta 89-1112_2.fq.gz hg19.fa.bwt s.marcescens_plas.fasta.amb e.coli.fasta hg19.fa.pac s.marcescens_plas.fasta.ann e.coli.fasta.amb hg19.fa.sa s.marcescens_plas.fasta.bwt e.coli.fasta.ann p.tolaasii.fasta s.marcescens_plas.fasta.pac e.coli.fasta.bwt p.tolaasii.fasta.amb s.marcescens_plas.fasta.sa e.coli.fasta.pac p.tolaasii.fasta.ann x.phaseoli.fasta e.coli.fasta.sa p.tolaasii.fasta.bwt x.phaseoli.fasta.amb GCF_023897955.1_iqSchGreg1.2_genomic.fa p.tolaasii.fasta.pac x.phaseoli.fasta.ann GCF_023897955.1_iqSchGreg1.2_genomic.fa.amb p.tolaasii.fasta.sa x.phaseoli.fasta.bwt GCF_023897955.1_iqSchGreg1.2_genomic.fa.ann s.marcescens_chr.fasta x.phaseoli.fasta.pac GCF_023897955.1_iqSchGreg1.2_genomic.fa.bwt s.marcescens_chr.fasta.amb x.phaseoli.fasta.sa GCF_023897955.1_iqSchGreg1.2_genomic.fa.pac s.marcescens_chr.fasta.ann GCF_023897955.1_iqSchGreg1.2_genomic.fa.sa s.marcescens_chr.fasta.bwt

However, once I tried to run the command, i got this error: $ fastq_screen --aligner bwa --conf 1.conf --threads 8 89-1112_1.fq.gz 89-1112_2.fq.gz Using fastq_screen v0.15.3 Reading configuration from '1.conf' Using '/home/DataDisk/th_data/software/envs/bwa' as BWA path Skipping DATABASE 'x.ph' since no BWA index was found at '/home/DataDisk/th_data/workplace/de-contamination/database_custom/x.phaseoli' Skipping DATABASE 's.mp' since no BWA index was found at '/home/Datadisk/th_data/workplace/de-contamination/database_custom/s.marcescens_plas' Skipping DATABASE 's.mc' since no BWA index was found at '/home/Datadisk/th_data/workplace/de-contamination/database_custom/s.marcescens_chr' Skipping DATABASE 'p.to' since no BWA index was found at '/home/Datadisk/th_data/workplace/de-contamination/database_custom/p.tolaasii' Skipping DATABASE 'homo' since no BWA index was found at '/home/Datadisk/th_data/workplace/de-contamination/database_custom/hg19' Skipping DATABASE 's.gr' since no BWA index was found at '/home/Datadisk/th_data/workplace/de-contamination/database_custom/GCF_023897955.1_iqSchGreg1.2_genomic' Skipping DATABASE 'e.coli' since no BWA index was found at '/home/Datadisk/th_data/workplace/de-contamination/database_custom/e.coli' Using 8 threads for searches No reference genomes were configured, please adjust configuration.

I really wish to know what happen and thanks so much for your help :)

[Linnaeus001]

maybe i should put them into different folders?

[Linnaeus001]

okay... i got the same problem as issue 61 did. Now it's done

[StevenWingett]

Hi,

Is this working now?

Regards, Steven

[Linnaeus001]

Hi,

Is this working now?

Regards, Steven

yeah it work now, the DATABASE work path isn't complete, i forgot to add .fa at the end of the path