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99.98 298629 298629 0 0 U 0 unclassified
0.02 63 0 2852 1524 R 1 root
0.02 63 0 2852 1524 D 10239 Viruses
0.02 61 0 2372 1261 D1 2731341 Duplodnaviria
0.02 61 0 2372 1261 K 2731360 Heunggongvirae
0.02 61 0 2323 1235 P 2731618 Uroviricota
0.02 61 5 2323 1235 C 2731619 Caudoviricetes
0.01 26 0 654 436 O 1978007 Crassvirales
0.01 22 0 530 337 F 2942966 Suoliviridae
0.01 22 4 520 332 F1 2942975 Oafivirinae
99.97 412426 412426 0 0 U 0 unclassified
0.03 129 0 5007 2682 R 1 root
0.03 129 1 5007 2682 D 10239 Viruses
0.03 125 0 4402 2358 D1 2731341 Duplodnaviria
0.03 125 0 4402 2358 K 2731360 Heunggongvirae
0.03 125 0 4361 2334 P 2731618 Uroviricota
0.03 125 10 4361 2334 C 2731619 Caudoviricetes
0.01 51 0 1589 1190 O 1978007 Crassvirales
0.01 42 0 1168 883 F 2942966 Suoliviridae
0.01 42 3 1155 874 F1 2942975 Oafivirinae
#mpa_vOct22_CHOCOPhlAnSGB_202212
#/usr/local/bin/metaphlan --nproc 6 --input_type fastq 2613_ERR5766181.unmapped.fastq.gz --bowtie2out 2613_se_metaphlan4-db.metaphlan.bowtie2out.txt --bowtie2db metaphlan4 --index mpa_vOct22_CHOCOPhlAnSGB_202212 --biom 2613_se_metaphlan4-db.metaphlan.biom --output_file 2613_se_metaphlan4-db.metaphlan_profile.txt
#265493 reads processed
#SampleID Metaphlan_Analysis
#clade_name NCBI_tax_id relative_abundance additional_species
k__Bacteria 2 69.12967
k__Archaea 2157 30.87033
k__Archaea|p__Euryarchaeota 2157|28890 30.87033
k__Bacteria|p__Actinobacteria 2|201174 26.69296
k__Bacteria|p__Firmicutes 2|1239 21.84616
#mpa_vOct22_CHOCOPhlAnSGB_202212
#/usr/local/bin/metaphlan --nproc 6 --input_type fastq 2612.merged.fastq.gz --bowtie2out 2612_se_metaphlan4-db.metaphlan.bowtie2out.txt --bowtie2db metaphlan4 --index mpa_vOct22_CHOCOPhlAnSGB_202212 --biom 2612_se_metaphlan4-db.metaphlan.biom --output_file 2612_se_metaphlan4-db.metaphlan_profile.txt
#707440 reads processed
#SampleID Metaphlan_Analysis
#clade_name NCBI_tax_id relative_abundance additional_species
k__Bacteria 2 89.92809
k__Archaea 2157 10.07191
k__Bacteria|p__Bacteroidetes 2|976 31.03622
k__Bacteria|p__Actinobacteria 2|201174 29.64669
k__Bacteria|p__Firmicutes 2|1239 27.90168
@MajoroMask
MajoroMask / gist:9c7f164ce42a9f99c537c60254f39a53
Created October 7, 2023 06:58
Error message from `taxpasta merge`
╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│ /usr/local/lib/python3.11/site-packages/taxpasta/infrastructure/cli/merge.py │
│ :448 in merge │
│ │
│ 445 │ │ logger.critical("Less than two profiles are without errors. No │
│ 446 │ │ raise typer.Exit(code=1) │
│ 447 │ │
│ ❱ 448 │ result = handling_app.merge_samples(samples, wide_format) │
│ 449 │ │
│ 450 │ if valid_output_format is not WideObservationTableFileFormat.BIOM: │
@MajoroMask
MajoroMask / gist:e66f8a6160cb355ce7a6f97ef0a29474
Created October 5, 2023 02:11
my test log of taxprofiler/taxprofiler
[7f/f642cb] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR (test-db-ganon.tar.gz)
[a2/c3dccb] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)
[f5/f3abe6] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:SHORTREAD_HOSTREMOVAL:BOWTIE2_BUILD (genome.fasta)
[46/232b02] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR (test-db-centrifuge.tar.gz)
[e7/c10e2f] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR (metaphlan_database.tar.gz)
[75/06f0ba] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR (testdb-kraken2.tar.gz)
[e2/c62873] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR (test-db-kmcp.tar.gz)
[57/232ab0] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR (metaphlan4_database.tar.gz)
[8e/4f267f] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:DB_CHECK:UNTAR (kaiju.tar.gz)
[27/a343eb] Submitted process > NFCORE_TAXPROFILER:TAXPROFILER:LONGREAD_HOSTREMOVAL: