Abnormal fastq lines
2
0
Entering edit mode
4 months ago
jaqx008 ▴ 110

Hello all, I obtained this SRA files from ncbi. Something appears to be off with the third lines and I am not sure what but its causing bowtie to throw the following error: How can I fix this?

Bowtie error:

Saw ASCII character Saw ASCII character Saw ASCII character Saw ASCII character Saw ASCII character Saw ASCII character Saw ASCII character Saw ASCII character 10Saw ASCII character 10 but expected 33-based Phred qual.Saw ASCII character 10 but expected 33-based Phred qual. 10 but expected 33-based Phred qual.Saw ASCII character 1010 but expected 33-based Phred qual. Saw ASCII character 1010 but expected 33-based Phred qual.10 but expected 33-based Phred qual.10 but expected 33-based Phred qual.10 but expected 33-based Phred qual.Saw ASCII character 10 but expected 33-based Phred qual.

Saw ASCII character  10terminate called recursively



 but expected 33-based Phred qual.  but expected 33-based Phred qual.Saw ASCII character terminate called after throwing an instance of 'int10' terminate called recursively


Saw ASCII character  terminate called recursively 10 but expected 33-based Phred qual. terminate called recursively Saw ASCII character 10 but expected 33-based Phred qual.terminate called recursively terminate called recursively  but expected 33-based Phred qual. Saw ASCII character 10 but expected 33-based Phred qual. terminate called recursively  but expected 33-based Phred qual.(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

Fastq-file:

 @DRR032677.1 1 length=101
AAATGCTCAACCTGCAGATGTGAATTGTTACGACAAAACTTCCTATCACGCCAATGCCCAGTTCTCCAGAGTGTTTCCATTTTAAACCTTCTTCAGCCCCC
+DRR032677.1 1 length=101
@@@FFDFFHHDFHBHJJGIIIIHGJICFHEHEEF6:@FHID9DH>@FGDDCHGE@AGIECEIIIIGE>A;?;@.;..>@CCDEECCCCCC;AC>@CDC?B?
fastq-file-error SRR-flile mapping-error • 533 views
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Entering edit mode
4 months ago
GenoMax 110k

Try downloading fastq file from EBI-ENA and see if that fares better.

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You are right. They looked just fine on EBI-ENA. Thanks a bunch.

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Entering edit mode
4 months ago

What's visible looks fine. ASCII 10 is a line feed. You might need too investigate how to examine and remove white spaces from files.

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Thanks for your suggestion. I was able to resolve it using GenoMax suggestion. Thank you

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