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No warning for truncated fastq.gz file #264

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smoretti opened this issue Jun 24, 2020 · 0 comments
Open

No warning for truncated fastq.gz file #264

smoretti opened this issue Jun 24, 2020 · 0 comments

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@smoretti
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Hi
I use fastp 0.19.5 on Linux and have an issue with truncated fastq.gz files.
Sometimes downloaded fastq.gz files are incomplete, truncated and fastp processes them as if they were complete.

For paired-end reads truncation implies that both fastq files have different numbers of reads.
On a truncated fastq.gz file the zcat command returns something like:

$ zcat SRRaaa_1.fastq.gz >/dev/null
gzip: SRRaaa_1.fastq.gz: invalid compressed data--crc error
gzip: SRRaaa_1.fastq.gz: invalid compressed data--length error

Here is my command:
fastp -i SRRaaa_1.fastq.gz -I SRRaaa_2.fastq.gz --json SRRaaa.fastp.json --html SRRaaa.fastp.html --thread 2 > SRRaaa.fastp.log 2>&1

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