[2024-01-24 11:35:10,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:10,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:10,013] [INFO] DQC Reference Directory: /var/lib/cwl/stge40d23a6-d4bd-4abc-9e38-bc67e5a081aa/dqc_reference
[2024-01-24 11:35:11,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:11,385] [INFO] Task started: Prodigal
[2024-01-24 11:35:11,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg91b64f5c-2cbd-485c-ac36-57f3a45cf898/GCF_014647335.1_ASM1464733v1_genomic.fna.gz | prodigal -d GCF_014647335.1_ASM1464733v1_genomic.fna/cds.fna -a GCF_014647335.1_ASM1464733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:36,980] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:36,981] [INFO] Task started: HMMsearch
[2024-01-24 11:35:36,981] [INFO] Running command: hmmsearch --tblout GCF_014647335.1_ASM1464733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge40d23a6-d4bd-4abc-9e38-bc67e5a081aa/dqc_reference/reference_markers.hmm GCF_014647335.1_ASM1464733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:37,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:37,284] [INFO] Found 6/6 markers.
[2024-01-24 11:35:37,326] [INFO] Query marker FASTA was written to GCF_014647335.1_ASM1464733v1_genomic.fna/markers.fasta
[2024-01-24 11:35:37,326] [INFO] Task started: Blastn
[2024-01-24 11:35:37,326] [INFO] Running command: blastn -query GCF_014647335.1_ASM1464733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge40d23a6-d4bd-4abc-9e38-bc67e5a081aa/dqc_reference/reference_markers.fasta -out GCF_014647335.1_ASM1464733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:37,935] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:37,939] [INFO] Selected 7 target genomes.
[2024-01-24 11:35:37,940] [INFO] Target genome list was writen to GCF_014647335.1_ASM1464733v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:37,943] [INFO] Task started: fastANI
[2024-01-24 11:35:37,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b64f5c-2cbd-485c-ac36-57f3a45cf898/GCF_014647335.1_ASM1464733v1_genomic.fna.gz --refList GCF_014647335.1_ASM1464733v1_genomic.fna/target_genomes.txt --output GCF_014647335.1_ASM1464733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:46,775] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:46,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge40d23a6-d4bd-4abc-9e38-bc67e5a081aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:46,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge40d23a6-d4bd-4abc-9e38-bc67e5a081aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:46,783] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:35:46,783] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:46,783] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	100.0	1581	1583	95	conclusive
Butyricimonas faecihominis	strain=CCUG 65562	GCA_008830385.1	1472416	1472416	type	True	99.9986	1570	1583	95	conclusive
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	99.998	1578	1583	95	conclusive
Butyricimonas paravirosa	strain=DSM 105722	GCA_011927845.1	1472417	1472417	type	True	94.796	1193	1583	95	below_threshold
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	94.7893	1196	1583	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	91.205	1088	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,785] [INFO] DFAST Taxonomy check result was written to GCF_014647335.1_ASM1464733v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:46,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:46,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:46,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge40d23a6-d4bd-4abc-9e38-bc67e5a081aa/dqc_reference/checkm_data
[2024-01-24 11:35:46,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:46,836] [INFO] Task started: CheckM
[2024-01-24 11:35:46,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647335.1_ASM1464733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647335.1_ASM1464733v1_genomic.fna/checkm_input GCF_014647335.1_ASM1464733v1_genomic.fna/checkm_result
[2024-01-24 11:36:56,733] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:56,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:56,758] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:56,759] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:56,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647335.1_ASM1464733v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:56,760] [INFO] Task started: Blastn
[2024-01-24 11:36:56,760] [INFO] Running command: blastn -query GCF_014647335.1_ASM1464733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge40d23a6-d4bd-4abc-9e38-bc67e5a081aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647335.1_ASM1464733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:57,561] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:57,565] [INFO] Selected 7 target genomes.
[2024-01-24 11:36:57,565] [INFO] Target genome list was writen to GCF_014647335.1_ASM1464733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:57,572] [INFO] Task started: fastANI
[2024-01-24 11:36:57,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b64f5c-2cbd-485c-ac36-57f3a45cf898/GCF_014647335.1_ASM1464733v1_genomic.fna.gz --refList GCF_014647335.1_ASM1464733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647335.1_ASM1464733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:05,602] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:05,613] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:05,614] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014647335.1	s__Butyricimonas faecihominis	100.0	1581	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	conclusive
GCF_011927845.1	s__Butyricimonas paravirosa	94.796	1193	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.86	97.78	0.90	0.83	11	-
GCF_000519105.1	s__Butyricimonas virosa	91.2772	1066	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	-
GCA_019117165.1	s__Butyricimonas faecavium	87.7077	742	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991565.1	s__Butyricimonas faecalis	87.609	917	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.78	97.96	0.89	0.85	6	-
GCA_900761485.1	s__Butyricimonas sp900761485	83.7134	779	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003479425.1	s__Butyricimonas sp003479425	81.458	856	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:05,615] [INFO] GTDB search result was written to GCF_014647335.1_ASM1464733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:05,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:05,619] [INFO] DFAST_QC result json was written to GCF_014647335.1_ASM1464733v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:05,620] [INFO] DFAST_QC completed!
[2024-01-24 11:37:05,620] [INFO] Total running time: 0h1m56s