Hello,
I have used qiime2 for taxonomic classification using SILVA 138 database. I have run the command qiime feature-classifier-consensus classify-consunses-vsearch but it constently getting killed after matching unique query sequences: 99.78%.
I have used the same command previously for different samples and got the results, but this time I am facing the difficulty.
Can someone please help me out?
Thanks for any help you could provide me.
Have a good day,
Ankita Maddheshiya
Hi @Ankita_Maddheshiya,
Welcome to the QIIME 2 Forum!
Can you please re-run your command including the --verbose parameter, and then copy/paste the exact command you ran and the complete output here?
Thanks!
Sure, here is the command I used:
$qiime feature-classifier classify-consensus-vsearch --i-query rep-seqs.qza --i-reference-reads silva-138-99-seqs.qza --i-reference-taxonomy silva-138-99-tax.qza --p-threads 35 --output-dir vsearch_taxonomy --verbose
The output was:
Please find the attached files and let me know if you need any additional information
Thanks,
Ankita
Hello @Ankita_Maddheshiya,
Would you mind copying and pasting this output from the terminal and posting it here as text instead? Although it looks like you got everything with the pictures, it's a little hard to tell, and more difficult to read.
Thanks.
Hello @colinvwood,
Here is the output I got after running the command.
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: vsearch --usearch_global /tmp/qiime2/bmgu/data/ec24421e-a7ec-45d5-a153-c8a29309465f/data/dna-sequences.fasta --id 0.8 --query_cov 0.8 --strand both --maxaccepts 10 --maxrejects 0 --db /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta --threads 35 --output_no_hits --blast6out /tmp/q2-BLAST6Format-bw94_0z1
vsearch v2.14.0_linux_x86_64, 125.6GB RAM, 40 cores
Reading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file 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/tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequencReading file /tmp/qiime2/bmgu/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta 100%
636194718 nt in 436680 seqs, min 900, max 3983, avg 1457
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Searching 100%
Matching unique query sequences: 33646 of 33720 (99.78%)
Killed
Hello @Ankita_Maddheshiya,
This could be a memory issue, have you tried running this command with fewer threads?
What version of qiime are you using? I found this post where someone claims to have fixed this problem by changing from 2022.8 to a different version.
Hello @colinvwood,
I have also tried running the command by exporting the temp directory to an external HDD, so I don't think its a memory issue.
I am currently using 2022.8 version. I will use a different version and see if my issue is getting resolved or not.
Thank you so much for your response.
Regards,
Ankita
Hello @Ankita_Maddheshiya,
I meant the RAM kind of memory. 35 threads is quite a lot, so try lowering that if switching qiime versions doesn't help.
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