paired reads have different names (bwa-mem)
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Entering edit mode
5.2 years ago
AISHA ▴ 120

Hi, I am experiencing a problem while running BWA mem on paired end fastq file downloaded from NCBI SRA. When I ran BWA-mem it gives an error like:

[mem_sam_pe] paired reads have different names: "SRR3239806.1.1", "SRR3239806.1.2"

Example Fastq file:

@SRR3239806.1.1 1 length=100 TTGTGTAGGGTGGGTAGGCTCCATGTTTCCCAGCAAAGCTGGAGACATACAGACTACCTGGTGTTACATTTATTTCAGTGCCTCCTGAGTGTCTCTAAAT +SRR3239806.1.1 1 length=100 B@CDDFEFFHFFFI@GHIJGIJJJIJIIJJJGGHHIIIJJJJHIIGEHGIJIIIEGIGGHI@A=AHHFDEFFFFFEDEEECCDDDDD3<@CCCDDAC@CC

@SRR3239806.1.2 1 length=100

@SRR3239806.2.1 2 length=100

@SRR3239806.2.2 2 length=100

(I've just pasted the headers for the sake of brevity.) Can anyone explain how can I fix this error?

next-gen • 14k views
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Is it actually an error or just a warning? Did you download the fastq files or convert them with SRAtools?

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Its an error. I downloaded fastq file directly. It was a single file.

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Entering edit mode
5.1 years ago
mmfansler ▴ 410

It appears that when the FASTQ file was dumped from the SRA file, the -I | --readids option was used in fastq-dump. BWA requires that paired reads have completely identical read names, so this option isn't compatible.

You could process the file(s) to remove those appended .(1|2)s,

sed -E "s/^((@|\+)SRR[^.]+\.[^.]+)\.(1|2)/\1/" SRR3239806.fastq > SRR3239806.fixed.fastq


or you could rerun the dump from SRA to FASTQ (which could be just as fast if the SRA is cached):

fastq-dump --split-files SRR3239806


or, if you'd like to keep working with an interleaved file:

fastq-dump --split-spot SRR3239806

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Entering edit mode

I had the same issue having used the SRA fastq-dump - but without access to the sra file and the files are fastq.gz - I came up with:

gunzip -c test.fastq.gz | sed -E 's/(^[@+]SRR[0-9]+\.[0-9]+)\.[12]/\1/' | gzip -c > test.fixed.fastq.gz


It's a bit slow on a 4GB file but it worked.

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5.2 years ago
GenoMax 118k

I suggest you download the fastq files directly from EBI-ENA where you will find the two reads (R1/R2) in separate files.

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Interleaved files are not a problem for BWA - that's what the -p flag is for.

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Yes! I downloaded the interleaved fastq file. Isn't there any method to remove the above-mentioned error in the file?

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Reads you downloaded are using modified SRA headers (if you used fastq-dump to get the data you should have used the -F option to retrieve original Illumina headers. You could mess with the file you have but I suggest that you get the fastq's from ENA or do a new fastq-dump.

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3.9 years ago
Sasha Fokin ▴ 80

This is also possible when the fourth and second lines (in fastq file) has differ length. In this case, the Line1 (sequence identifier) of the fastq can be correct

But the program will return the same error:

[mem_sam_pe] paired reads have different names: "@E00576:153:HK75TCCXY:2:1101:23470:1713"

for example

first read (line 2 and line 4 has differ length - and that's the problem):

@E00576:153:HK75TCCXY:2:1101:23470:1713 2:N:0:NTTACTCG+AGGCTATA
AATAATAATAAAATAAAATAATGTGCTATAAGGTCTTATTTGCAAGCTTCATGGTAGCCTCAATTAAACAAACCTGCAAACAAAAAATAAAAAATAAAAA
+
JJJJFFJJFFJJFJJJJJJJJJJJJFJFJJAFFJJJJFJJAFJJFAJF<JJJF<--7A<F<F7FJJFJJJJFAFA)7<<F<---7-<7AFJJFJ<<FFJ


@E00576:153:HK75TCCXY:2:1101:23470:1713 1:N:0:NTTACTCG+AGGCTATA
GCAGGCTTCTGTGAAGGTGATTTTCTCTGGTGGAATGTTTTAATTTCCTGCTTTTTATTTTTTTTTTCTTGGTTGCAGTTTTGTTTAATTGAGGATACCATGAAGTTTGCAAATAAGACCTTATAGCATTTTATTTTATTTTATTATTAT
+
AAAFFJJJJJJJJFAFJJJ-<-FFJFJFJJJFJJJJJFJ<F-JA-J-FFJJJJJ-F<-FJJJJ<JFJF<JFAAF-A-F-AAJ<FFJA-<A--A-7AF---7<-77-7FJ7<7FJJ<AJA--<FA<-7---7J7AJAJ-<FFA-7FAAFAF

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That is not true in my experience. When using these two lines with bwa-mem 0.7.16a, it returns

[W::bseq_read] the 1st file has fewer sequences.

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@ATpoint, it's interesting, maybe I did not use the most stable version: 0.7.17-r1194-dirty