Question: Centrifuge - Error: reads file does not look like a FASTQ file
0
gravatar for richard
4 months ago by
richard0
richard0 wrote:

I am getting the error that my fastq files are not actual fastq files from Centrifuge. Not sure what is wrong with my files. They seem like normal fastq files and have run successfully through other metagenomic pipelines like metaphlan2, but fail with Centrifuge. Here is prep & my command:

nufile=echo $file | cut -d '_' -f 1
if [[ $file == "${nufile}_1.fastq" ]]; then

    echo "Now processing: $nufile"

    centrifuge -x /home/ubuntu/GTDB_r89_54k/gtdb_r89_54k \
        -1 /home/ubuntu/HMP2_MGX/reads/${nufile}_1.fastq \
        -2 /home/ubuntu/HMP2_MGX/reads/${nufile}_2.fastq \
        -q -S ${nufile}_classification \
        --report-file ${nufile}_report.tsv -t -p 32

Here is a sample of my fastq files:

@CAPPMANXX170326:7:1101:10001:90412/1
TTCTAAATGATCAAGACATATTAAATGCTCTATTATACGACCAAAAGGTACTAATAGATATAAAGTGG
+
BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFF
@CAPPMANXX170326:7:1101:10004:75175/1
GCAGGGAGAAGACCGCTGTATTGTGGCCATCGAAGTGAACGGCGAAGCAAAGAAGTTCTTCACCAACAGCGAGGAAATGAAG
+
/BBBBFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFF
@CAPPMANXX170326:7:1101:10005:95028/1
CTCTTAACACTTATGAGTGGTTCCCTAAAAATACAGATCCATATCCGGTAGAGGCTGTTGATGCTGAATTTATTACCTCGGATATACTTACTTTGCCTGAT

Here is my error:

Time loading forward index: 00:06:00 Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' (ERR): centrifuge-class died with signal 6 (ABRT) (core dumped) `

Any ideas on what could be causing this problem ?

ADD COMMENTlink modified 4 months ago by h.mon30k • written 4 months ago by richard0
4

Shouldn't that be nufile=$(echo $file | cut -d '_' -f 1)?

ADD REPLYlink written 4 months ago by cschu1812.3k

sure, but thats not the issue. It is in parentheses in the actual code, which I couldn't post here. The issue is that centrifuge is throwing an error about my fastq files

ADD REPLYlink written 4 months ago by richard0
1

Can you run validateFiles from Kent utils on your fastq files to see if you can identify any issues: C: Viewing and editing FASTQ files

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax85k

Thanks, will do and will get back to you

ADD REPLYlink written 4 months ago by richard0

Figured it out, Something was corrupted in my reverse reads, going to re-download them. Thanks again!

ADD REPLYlink written 4 months ago by richard0
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