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Format error for filterBlastInfo.sh #6

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KyoHiki opened this issue Mar 14, 2023 · 1 comment
Closed

Format error for filterBlastInfo.sh #6

KyoHiki opened this issue Mar 14, 2023 · 1 comment

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@KyoHiki
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KyoHiki commented Mar 14, 2023

Hi,

When I run filterBlastInfo.sh with paired end option, I found the following error.
Although the error said "Paired end should be numbered as xxx/1 and xxx/2", the name of blast table file was like "XXX1.table" or "XXXX1_vs_bacteria.table". What should I do to address this error?

filterBlastInfo.sh -i /media/.../decontaminer/RESULTS/BACTERIA

--------------output--------------
-- FILTERING BLAST RESULTS --

INFO: paired/single end flag -s not specified. PAIRED END assumed (default option).
INFO: organism type flag -V not specified. O(thers) assumed (default option).

  • PROCESSING DETAILS
    INFO: processing PAIRED END data.
    INFO: processing NON virus alignments
    Processing file /media/.../decontaminer/RESULTS/BACTERIA/0_unmapped.1_vs_bacteria.table

Using L=read length G =0 M=0
Processing...

Format error on paired end names! Paired end should be numbered as xxx/1 and xxx/2 where xxx is the name of the query
--------------↑output--------------

Before filterBlastInfo.sh, I performed decontaMiner.sh using the paried end fastq files (0_unmapped.1.fastq, 0_unmapped.2.fastq). And in the directly RESULTS/BACTERIA, the files like 0_unmapped.1_vs_bacteria were generated.

@KyoHiki
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KyoHiki commented Mar 15, 2023

Oh, I found the previous issue on the same error.

@KyoHiki KyoHiki closed this as completed Mar 15, 2023
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