The Unable to find proper fastq read pair in the format *_1.fastq and *_2.fastq

[jolespin]

I'm providing the paired reads buts not recognizing my reads. Even when I interleave the reads and explicitly set --interleaved it doesn't work.

There's no error messages.

Do you have any idea what it could be?

metawrap binning -o INITIAL_BINNING -t 4 -a ../metaspades_output/contigs.fasta --maxbin2 --metabat2 --concoct ../bbmap_output/mapped_R1.fq ../bbmap_output/mapped_R2.fq

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-----                                           Entered read type: paired                                          -----
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-----                  Unable to find proper fastq read pair in the format *_1.fastq and *_2.fastq                 -----
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Usage: metaWRAP binning [options] -a assembly.fa -o output_dir readsA_1.fastq readsA_2.fastq ... [readsX_1.fastq readsX_2.fastq]
Note1: Make sure to provide all your separately replicate read files, not the joined file.
Note2: You may provide single end or interleaved reads as well with the use of the correct option
Note3: If the output already has the .bam alignments files from previous runs, the module will skip re-aligning the reads

Options:

    -a STR          metagenomic assembly file
    -o STR          output directory
    -t INT          number of threads (default=1)
    -m INT      amount of RAM available (default=4)
    -l INT      minimum contig length to bin (default=1000bp). Note: metaBAT will default to 1500bp minimum

    --metabat2      bin contigs with metaBAT2
    --metabat1  bin contigs with the original metaBAT
    --maxbin2   bin contigs with MaxBin2
    --concoct   bin contigs with CONCOCT

    --universal use universal marker genes instead of bacterial markers in MaxBin2 (improves Archaea binning)
    --run-checkm    immediately run CheckM on the bin results (requires 40GB+ of memory)
    --single-end    non-paired reads mode (provide *.fastq files)
    --interleaved   the input read files contain interleaved paired-end reads

real    0m0.084s
user    0m0.023s
sys 0m0.033s

[ursky]

Like the error says, the program expect the read file names to be in the *_1.fastq and *_2.fastq format.

[jolespin]

Yup, that was it thanks! I thought it was giving an example. Does it expect a particular format with interleaved read names?

[ursky]

I believe its .fastq.

[sashulkaSh]

do I need to unzip the archive?????? if my files in format *.fq.gz

I believe its .fastq.

[sashulkaSh]

It is very uncomfortable...

[jianshu93]

Hi all,

Some trick, just soft link a new name with .fastq as suffix, to the .fasta.gz file, it works!

Jianshu

[hellopeccat]

Hi all,

Some trick, just soft link a new name with .fastq as suffix, to the .fasta.gz file, it works!

Jianshu

Great job! I address it with Jianshu's idea, and many thanks to the help.