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billzt / MiFish

This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers
https://mitofish.aori.u-tokyo.ac.jp/mifish/
GNU General Public License v3.0
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Issues on Analysing Fish eDNA Data #11

Closed Tricksie28 closed 4 months ago

Tricksie28 commented 6 months ago

Good day!

I have issues regarding analyzing my fish eDNA data on your website. It took hours to run it. It’s not yet analyzed. It’s almost 24 hrs but it is still running. Can you lend me a help on how can I troubleshoot my data? Thank you. Fish_eDNA_10_1.fastq.gz Fish_eDNA_10_2.fastq.gz Fish_eDNA_11_1.fastq.gz Fish_eDNA_11_2.fastq.gz

billzt commented 6 months ago

Hi @Tricksie28

Thank you for your issue.

The main reason is that your sequences are not from fish, but from bacteria. The analysis process has already stopped due to too few valid sequences.

I test the first ten reads of Fish_eDNA_10_1.fastq.gz

test.first10reads.fa.txt

Using https://blast.ncbi.nlm.nih.gov/Blast.cgi to search them against nt_prok + nt_euk, I found that they are all from bacteria, fungi, or other micro-organisms.

For example, the first read seems originated from bacteria

>M05881:549:000000000-LB3K3:1:1102:15045:1171 1:N:0:GCCATATAAC+ACACAATATC
GTCGGTAAAACTCGTGCCAGCAGCCGCGGTAATACGGAGGGTCCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTTGTCAGTCAGATGTGAAAGCCCAGGGCTCAACCTTGGAACTGCACCTGATACTGCAAGACTAGAGTACAATAGAGGGGAGTGGAATTTCCGGTGTAGCGGTGAAATGCGTAGAGATCGGAAGGAACACCAGTGGCGAAGGCGACTCCCTGGATTGATACTGTCACTGAGGTGCGAAAGCGTGGGGAGGAAACTGGGATTAGATACCCCACT

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