Error: record does not start with '@'
1
0
Entering edit mode
mafusa20 • 0
@mafusa20-19278
Last seen 5.9 years ago

i'm do the pipeline of ASV for 16s analysis with demultiplexed files with .fq format.

> list.files(path)
 [1] "DAtos demulteplixados.Rproj"         "filtered"                           
 [3] "Mock_S280_L001_R1_001.fastq"         "Mock_S280_L001_R2_001.fastq"        
 [5] "SAMPLE1_1.fq"                        "SAMPLE10_1.fq"                      
 [7] "SAMPLE11_1.fq"                       "SAMPLE12_1.fq"                      
 [9] "SAMPLE13_1.fq"                       "SAMPLE14_1.fq"                      
[11] "SAMPLE15_1.fq"                       "SAMPLE2_1.fq"                       
[13] "SAMPLE3_1.fq"                        "SAMPLE4_1.fq"                       
[15] "SAMPLE5_1.fq"                        "SAMPLE6_1.fq"                       
[17] "SAMPLE7_1.fq"                        "SAMPLE8_1.fq"                       
[19] "SAMPLE9_1.fq"                        "silva_nr_v128_train_set.fa.gz"      
[21] "silva_species_assignment_v128.fa.gz"
>fnFs <- sort(list.files(path, pattern="_1.fq", full.names = TRUE))
> sample.names <- sapply(strsplit(basename(fnFs), "_"), `[`, 1)

> sample.names
 [1] "SAMPLE1"  "SAMPLE10" "SAMPLE11" "SAMPLE12" "SAMPLE13" "SAMPLE14" "SAMPLE15" "SAMPLE2" 
 [9] "SAMPLE3"  "SAMPLE4"  "SAMPLE5"  "SAMPLE6"  "SAMPLE7"  "SAMPLE8"  "SAMPLE9" 
> plotQualityProfile(fnFs)
Error: record does not start with '@'

Help my please.

DADA2 .fq • 2.1k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

This error comes from the ShortRead package, and it means that your FASTQ files have non-standard names (which should start with an @). As an example (from the command line):

$ zcat 303422_S150_L002_R1_001.fastq.gz | head -n 4 
@A00177:32:HFVCFDMXX:2:1101:1108:1000 1:N:0:GTCAACAG+GTCAACAG <- Note that this is a correct seqname
NGGATGGATCACTGGGTGTGTGGCATAGTCCATGCTCTTAACCAGATTTGAACAGGAGAATGGCCACCTGGCCCAGGTAGAAGTAGATGAAGTGTTTGGTT
+
#FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFF

## now make a FASTQ with missing @

$ zcat 303422_S150_L002_R1_001.fastq.gz | sed  's/@//g'  | head -n 24 > tmp.fq
$ head -n 4 tmp.fq 
A00177:32:HFVCFDMXX:2:1101:1108:1000 1:N:0:GTCAACAG+GTCAACAG <- this is not!
NGGATGGATCACTGGGTGTGTGGCATAGTCCATGCTCTTAACCAGATTTGAACAGGAGAATGGCCACCTGGCCCAGGTAGAAGTAGATGAAGTGTTTGGTT
+
#FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFF


$ Rscript -e "suppressPackageStartupMessages(library(ShortRead)); qa('tmp.fq')"
Error: record does not start with '@'
Execution halted

So you need to figure out what the problems is with your FASTQ files.

ADD COMMENT

Login before adding your answer.

Traffic: 465 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6