[2024-01-24 10:47:06,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,604] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc3c113c-3d45-45c4-8fd4-fa1f476dc711/dqc_reference
[2024-01-24 10:47:12,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,804] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,805] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5e2ae4e-6d5e-4ed2-ae26-69d5927d369e/GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/cds.fna -a GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:27,637] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:27,638] [INFO] Task started: HMMsearch
[2024-01-24 10:47:27,638] [INFO] Running command: hmmsearch --tblout GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc3c113c-3d45-45c4-8fd4-fa1f476dc711/dqc_reference/reference_markers.hmm GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:27,947] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:27,949] [INFO] Found 6/6 markers.
[2024-01-24 10:47:27,997] [INFO] Query marker FASTA was written to GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:47:27,998] [INFO] Task started: Blastn
[2024-01-24 10:47:27,998] [INFO] Running command: blastn -query GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc3c113c-3d45-45c4-8fd4-fa1f476dc711/dqc_reference/reference_markers.fasta -out GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:28,833] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:28,838] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:28,838] [INFO] Target genome list was writen to GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:47:29,180] [INFO] Task started: fastANI
[2024-01-24 10:47:29,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5e2ae4e-6d5e-4ed2-ae26-69d5927d369e/GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna.gz --refList GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:42,843] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:42,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc3c113c-3d45-45c4-8fd4-fa1f476dc711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:42,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc3c113c-3d45-45c4-8fd4-fa1f476dc711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:42,860] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:42,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:42,860] [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
Pseudomonas zeshuii	strain=KACC 15471	GCA_900141925.1	1076620	1076620	type	True	100.0	1761	1763	95	conclusive
Pseudomonas asuensis	strain=JCM 13501	GCA_014646755.1	1825787	1825787	type	True	85.3311	1331	1763	95	below_threshold
Pseudomonas duriflava	strain=CGMCC 1.6858	GCA_007830155.1	459528	459528	type	True	79.9363	638	1763	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	78.1457	358	1763	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_012985915.1	237610	237610	suspected-type	True	78.132	363	1763	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	78.0019	359	1763	95	below_threshold
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	77.9373	352	1763	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	77.8525	350	1763	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	77.659	244	1763	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	77.5881	256	1763	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	77.5311	240	1763	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	77.5257	280	1763	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	77.5179	237	1763	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	77.3999	279	1763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:42,867] [INFO] DFAST Taxonomy check result was written to GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:47:42,868] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:42,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:42,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc3c113c-3d45-45c4-8fd4-fa1f476dc711/dqc_reference/checkm_data
[2024-01-24 10:47:42,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:42,930] [INFO] Task started: CheckM
[2024-01-24 10:47:42,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/checkm_input GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:48:29,862] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:29,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:29,889] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:29,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:29,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:48:29,890] [INFO] Task started: Blastn
[2024-01-24 10:48:29,890] [INFO] Running command: blastn -query GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc3c113c-3d45-45c4-8fd4-fa1f476dc711/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:31,391] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:31,395] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:31,396] [INFO] Target genome list was writen to GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:31,427] [INFO] Task started: fastANI
[2024-01-24 10:48:31,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5e2ae4e-6d5e-4ed2-ae26-69d5927d369e/GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna.gz --refList GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:46,019] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:46,035] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:46,035] [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_002091675.1	s__Pseudomonas_B luteola	97.9093	1562	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.05	97.34	0.90	0.85	19	conclusive
GCF_014646755.1	s__Pseudomonas_B asuensis	85.3375	1330	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830155.1	s__Pseudomonas_B duriflava	79.9332	638	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001518815.1	s__Pseudomonas_B oryzihabitans_E	78.0092	336	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.13	98.08	0.95	0.93	4	-
GCF_006384975.1	s__Pseudomonas_B psychrotolerans_B	77.9732	339	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730625.1	s__Pseudomonas_B oryzihabitans	77.9372	352	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.97	96.38	0.92	0.87	28	-
GCF_008807375.1	s__Pseudomonas_F lalkuanensis	77.8844	250	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005250615.1	s__Pseudomonas_B rhizoryzae	77.8449	352	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.30	97.74	0.93	0.89	15	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	77.8425	366	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCF_001512295.1	s__Pseudomonas_B sp001512295	77.835	356	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	77.8319	275	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009189165.1	s__Pseudomonas sp009189165	77.7474	266	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060885.1	s__Pseudomonas_E sp003060885	77.3415	216	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112645.1	s__Pseudomonas_E straminea	77.2041	259	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.94	0.94	2	-
GCF_002094795.1	s__Pseudomonas_E putida_K	77.1127	239	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:46,037] [INFO] GTDB search result was written to GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:46,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:46,041] [INFO] DFAST_QC result json was written to GCF_900141925.1_IMG-taxon_2663762797_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 10:48:46,041] [INFO] DFAST_QC completed!
[2024-01-24 10:48:46,041] [INFO] Total running time: 0h1m39s