Input query was recognized as database

[cv-1993]

Hi Jaebeom Kim,

Thanks for developing Metabuli.

I've just installed Metabuli version 1.0.9.2 using Mamba environment and downloaded the pre-built database refseq 224.
However, when I tried to run Metabuli, it seemed like the second read was recognized as the database. Please see the detail below:

Here is the command: metabuli classify rawReads/L017_1.fastq.gz rawReads/L017_2.fastq.gz databases/Metabuli/refseq224 metabuli --threads 90 --max-ram 700

Here is the output:

MMseqs Version:                                         1.0.9.2
Threads                                                 90
Sequencing type                                         2
Min. sequence similarity score                          0
Min. query coverage                                     0
Min. num. of cons. matches for non-euk. classification  4
Min. num. of cons. matches for euk. classification      9
Min. score for species- or lower-level classification.  0
Allowed extra Hamming distance                          0
Directory where the taxonomy dump files are stored
Mask residues                                           0
Mask residues probability                               0.9
RAM usage in GiB                                        700
Number of matches per query k-mer.                      4
Accession-level DB build/search                         0
Best * --tie-ratio is considered as a tie               0.95
Not storing k-mer's redundancy. Keep it as 1.           0
Print lineage information                               0

Input database "rawReads/L017_2.fastq.gz" has the wrong type (Generic)
Allowed input:
- Directory

Thanks for your help to solve this issue.

[jaebeom-kim]

Please add a job name after outdir (matabuli in your case). I hope it solves the problem. 2025년 1월 24일 (금) 오후 4:48, cv-1993 ***@***.***>님이 작성:

…

Hi Jaebeom Kim, Thanks for developing Metabuli. I've just installed Metabuli version 1.0.9.2 using Mamba environment and downloaded the pre-built database refseq 224. However, when I tried to run Metabuli, it seemed like the second read was recognized as the database. Please see the detail below: Here is the command: metabuli classify rawReads/L017_1.fastq.gz rawReads/L017_2.fastq.gz databases/Metabuli/refseq224 metabuli --threads 90 --max-ram 700 Here is the output: MMseqs Version: 1.0.9.2 Threads 90 Sequencing type 2 Min. sequence similarity score 0 Min. query coverage 0 Min. num. of cons. matches for non-euk. classification 4 Min. num. of cons. matches for euk. classification 9 Min. score for species- or lower-level classification. 0 Allowed extra Hamming distance 0 Directory where the taxonomy dump files are stored Mask residues 0 Mask residues probability 0.9 RAM usage in GiB 700 Number of matches per query k-mer. 4 Accession-level DB build/search 0 Best * --tie-ratio is considered as a tie 0.95 Not storing k-mer's redundancy. Keep it as 1. 0 Print lineage information 0 Input database "rawReads/L017_2.fastq.gz" has the wrong type (Generic) Allowed input: - Directory Thanks for your help to solve this issue. — Reply to this email directly, view it on GitHub <#113>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQK2QJNEHHUWE7LZ7W4YKUT2MHV4NAVCNFSM6AAAAABVZCWL4KVHI2DSMVQWIX3LMV43ASLTON2WKOZSHAYDQNZXHAZDOOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[cv-1993]

@jaebeom-kim Thanks for a quick response.
I've added jobid: metabuli classify rawReads/L017_1.fastq.gz rawReads/L017_2.fastq.gz databases/Metabuli/refseq224 metabuli --threads 90 --max-ram 700

However, I still got the same error:
`MMseqs Version: 1.0.9.2
Threads 90
Sequencing type 2
Min. sequence similarity score 0
Min. query coverage 0
Min. num. of cons. matches for non-euk. classification 4
Min. num. of cons. matches for euk. classification 9
Min. score for species- or lower-level classification. 0
Allowed extra Hamming distance 0
Directory where the taxonomy dump files are stored
Mask residues 0
Mask residues probability 0.9
RAM usage in GiB 700
Number of matches per query k-mer. 4
Accession-level DB build/search 0
Best * --tie-ratio is considered as a tie 0.95
Not storing k-mer's redundancy. Keep it as 1. 0
Print lineage information 0

Input database "./rawReads/L017_2.fastq.gz" has the wrong type (Generic)
Allowed input:

• Directory`

[jaebeom-kim]

Your command is the same as before. Could you add one more text like L017 next to between "metabuli" and "--threads"? 2025년 1월 24일 (금) 오후 6:28, cv-1993 ***@***.***>님이 작성:

…

@jaebeom-kim <https://github.com/jaebeom-kim> Thanks for a quick response. I've added jobid: metabuli classify rawReads/L017_1.fastq.gz rawReads/L017_2.fastq.gz databases/Metabuli/refseq224 metabuli --threads 90 --max-ram 700 However, I still got the same error: `MMseqs Version: 1.0.9.2 Threads 90 Sequencing type 2 Min. sequence similarity score 0 Min. query coverage 0 Min. num. of cons. matches for non-euk. classification 4 Min. num. of cons. matches for euk. classification 9 Min. score for species- or lower-level classification. 0 Allowed extra Hamming distance 0 Directory where the taxonomy dump files are stored Mask residues 0 Mask residues probability 0.9 RAM usage in GiB 700 Number of matches per query k-mer. 4 Accession-level DB build/search 0 Best * --tie-ratio is considered as a tie 0.95 Not storing k-mer's redundancy. Keep it as 1. 0 Print lineage information 0 Input database "./rawReads/L017_2.fastq.gz" has the wrong type (Generic) Allowed input: - Directory` — Reply to this email directly, view it on GitHub <#113 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQK2QJMWNO53QV6XMK3BJPL2MIBUDAVCNFSM6AAAAABVZCWL4KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMJSGA2TQMZWGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[cv-1993]

@jaebeom-kim
Thanks. The run started after adding JobID.
However, the run crashed after ~10min without any error. It seemed to require higher computational power.
We have 750 GB in RAM and 96 CPU cores. Isn't it sufficient?

Thanks.

[jaebeom-kim]

Your computing resource is enough. Could you send me all the printed logs? It helps me find where the error happens.

[cv-1993]

@jaebeom-kim

classify ./rawReads/L017_1.fastq.gz ./rawReads/L017_2.fastq.gz databases/Metabuli/refseq224 metabuli L017 --threads 90 --max-ram 700

Metabuli Version (commit):                              1.0.9.2
Threads                                                 90
Sequencing type                                         2
Min. sequence similarity score                          0
Min. query coverage                                     0
Min. num. of cons. matches for non-euk. classification  4
Min. num. of cons. matches for euk. classification      9
Min. score for species- or lower-level classification.  0
Allowed extra Hamming distance                          0
Directory where the taxonomy dump files are stored
Mask residues                                           0
Mask residues probability                               0.9
RAM usage in GiB                                        700
Number of matches per query k-mer.                      4
Accession-level DB build/search                         0
Best * --tie-ratio is considered as a tie               0.95
Not storing k-mer's redundancy. Keep it as 1.           0
Print lineage information                               0

DB name: refseq_release_224_prokaryote_virus_human
DB creation date: 2024-9-27
Loading the list for taxonomy IDs ... Done
Indexing query file ...Done
Total number of sequences: 67123704
Total read length: 20271358608nt
Extracting query metamers ...
Time spent for metamer extraction: 28
Sorting query metamer list ...
Time spent for sorting query metamer list: 14
Comparing query and reference metamers...
--match-per-kmer was increased to 8 and searching again...
Extracting query metamers ...
Time spent for metamer extraction: 17
Sorting query metamer list ...
Time spent for sorting query metamer list: 10
Comparing query and reference metamers...
--match-per-kmer was increased to 12 and searching again...
Extracting query metamers ...
Time spent for metamer extraction: 11
Sorting query metamer list ...
Time spent for sorting query metamer list: 6
Comparing query and reference metamers...

Up to this point, the run crashed and the terminal just shut down.