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fastq_screen error: Failed to calculate read length

Running it like this:

fastq_screen --conf $FASTQ_SCREEN_DATA/fastq_screen.conf --aligner bowtie2 --threads 6 03dpf.filtered.tagged.unmapped-1.fasta.gz

Runs into this error. I cannot seem to find any information about this.

Using fastq_screen v0.15.1
Reading configuration from '/FastQ_Screen_Genomes/fastq_screen.conf'
Adding database Human
Adding database Mouse
Adding database Rat
Adding database Drosophila
Adding database Worm
Adding database Yeast
Adding database Arabidopsis
Adding database Ecoli
Adding database rRNA
Adding database MT
Adding database PhiX
Adding database Lambda
Adding database Vectors
Adding database Adapters
Using 6 threads for searches
Option --subset set to 100000 reads
Processing 03dpf.filtered.tagged.unmapped-1.fasta.gz
Failed to calculate read length from 03dpf.filtered.tagged.unmapped-1.fasta.gz
Processing complete

The output file looks quite empty:

#Fastq_screen version: 0.15.1   #Aligner: bowtie2   #Reads in subset: 100000
Genome  #Reads_processed    #Unmapped   %Unmapped   #One_hit_one_genome %One_hit_one_genome #Multiple_hits_one_genome   %Multiple_hits_one_genome   #One_hit_multiple_genomes   %One_hit_multiple_genomes   Multiple_hits_multiple_genomes  %Multiple_hits_multiple_genomes

I am running this tool for the first time, so I could be missing something obvious.

fastq_screen
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written by firestar firestar

Failed to calculate read length from 03dpf.filtered.tagged.unmapped-1.fasta.gz

Based on the name it looks like this is a fasta input? As the name suggests fastq_screen is likely expecting fastq format input.

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written by GenoMax GenoMax

1 answer

From the documentation:

FastQ Screen allows you to screen a library of sequences in FastQ format

You're passing a .fasta file.

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written by Trivas • Trivas

Right. I completely overlooked that. Didn't even think that quality score would be that relevant for what this tool does.

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written by firestar firestar

You could convert the fasta file to include fake Q scores if you still want to use it as an input.

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written by GenoMax GenoMax

I created the .fasta from a BAM, so I am just going to go back to the BAM and convert that to a .fastq and see if that works. But good to know about fake Qs if I ever need that. Thanks :)

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written by firestar firestar

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