[2024-01-25 19:45:50,358] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:50,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:50,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2ffbadf-d7c6-473c-8ad9-872b1216f089/dqc_reference
[2024-01-25 19:45:51,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:51,511] [INFO] Task started: Prodigal
[2024-01-25 19:45:51,511] [INFO] Running command: gunzip -c /var/lib/cwl/stgb410bdc4-81b5-46df-8c64-862a25c1803e/GCF_001006485.1_ASM100648v1_genomic.fna.gz | prodigal -d GCF_001006485.1_ASM100648v1_genomic.fna/cds.fna -a GCF_001006485.1_ASM100648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:05,748] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:05,748] [INFO] Task started: HMMsearch
[2024-01-25 19:46:05,748] [INFO] Running command: hmmsearch --tblout GCF_001006485.1_ASM100648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2ffbadf-d7c6-473c-8ad9-872b1216f089/dqc_reference/reference_markers.hmm GCF_001006485.1_ASM100648v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:05,973] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:05,974] [INFO] Found 6/6 markers.
[2024-01-25 19:46:06,005] [INFO] Query marker FASTA was written to GCF_001006485.1_ASM100648v1_genomic.fna/markers.fasta
[2024-01-25 19:46:06,005] [INFO] Task started: Blastn
[2024-01-25 19:46:06,005] [INFO] Running command: blastn -query GCF_001006485.1_ASM100648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2ffbadf-d7c6-473c-8ad9-872b1216f089/dqc_reference/reference_markers.fasta -out GCF_001006485.1_ASM100648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:06,562] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:06,565] [INFO] Selected 23 target genomes.
[2024-01-25 19:46:06,565] [INFO] Target genome list was writen to GCF_001006485.1_ASM100648v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:06,579] [INFO] Task started: fastANI
[2024-01-25 19:46:06,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgb410bdc4-81b5-46df-8c64-862a25c1803e/GCF_001006485.1_ASM100648v1_genomic.fna.gz --refList GCF_001006485.1_ASM100648v1_genomic.fna/target_genomes.txt --output GCF_001006485.1_ASM100648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:20,189] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:20,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2ffbadf-d7c6-473c-8ad9-872b1216f089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:20,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2ffbadf-d7c6-473c-8ad9-872b1216f089/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:20,200] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:20,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:20,200] [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
Tannerella forsythia	strain=ATCC 43037	GCA_001006485.1	28112	28112	type	True	100.0	1050	1053	95	conclusive
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	76.6451	67	1053	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	76.6355	65	1053	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	76.5821	67	1053	95	below_threshold
Parabacteroides goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	76.389	56	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:20,202] [INFO] DFAST Taxonomy check result was written to GCF_001006485.1_ASM100648v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:20,203] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:20,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:20,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2ffbadf-d7c6-473c-8ad9-872b1216f089/dqc_reference/checkm_data
[2024-01-25 19:46:20,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:20,248] [INFO] Task started: CheckM
[2024-01-25 19:46:20,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001006485.1_ASM100648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001006485.1_ASM100648v1_genomic.fna/checkm_input GCF_001006485.1_ASM100648v1_genomic.fna/checkm_result
[2024-01-25 19:47:02,246] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:02,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:02,262] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:02,262] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:02,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001006485.1_ASM100648v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:02,263] [INFO] Task started: Blastn
[2024-01-25 19:47:02,263] [INFO] Running command: blastn -query GCF_001006485.1_ASM100648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2ffbadf-d7c6-473c-8ad9-872b1216f089/dqc_reference/reference_markers_gtdb.fasta -out GCF_001006485.1_ASM100648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:03,032] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:03,035] [INFO] Selected 23 target genomes.
[2024-01-25 19:47:03,035] [INFO] Target genome list was writen to GCF_001006485.1_ASM100648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:03,058] [INFO] Task started: fastANI
[2024-01-25 19:47:03,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgb410bdc4-81b5-46df-8c64-862a25c1803e/GCF_001006485.1_ASM100648v1_genomic.fna.gz --refList GCF_001006485.1_ASM100648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001006485.1_ASM100648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:18,177] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:18,183] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:18,183] [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_001006485.1	s__Tannerella forsythia	100.0	1050	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Tannerella	95.0	98.78	98.50	0.94	0.91	12	conclusive
GCF_003860135.1	s__Tannerella forsythia_A	88.3091	742	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Tannerella	95.0	97.92	97.92	0.85	0.85	2	-
GCF_000154105.1	s__Parabacteroides merdae	76.6628	64	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	-
GCF_004793765.1	s__Parabacteroides distasonis_A	76.4906	50	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.06	98.88	0.88	0.86	4	-
GCF_014287585.1	s__Parabacteroides sp014287585	76.434	75	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCA_017937385.1	s__Parabacteroides sp017937385	76.0882	54	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162725.1	s__Marseille-P3160 sp900162725	75.9905	50	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Marseille-P3160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552465.1	s__Parabacteroides sp900552465	75.5343	53	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.92	99.92	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:18,185] [INFO] GTDB search result was written to GCF_001006485.1_ASM100648v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:18,185] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:18,188] [INFO] DFAST_QC result json was written to GCF_001006485.1_ASM100648v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:18,188] [INFO] DFAST_QC completed!
[2024-01-25 19:47:18,188] [INFO] Total running time: 0h1m28s