[2024-01-24 15:19:49,221] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:49,223] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:49,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg66feb33d-6f44-45f7-9dcb-604b7bac2d30/dqc_reference
[2024-01-24 15:19:50,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:50,513] [INFO] Task started: Prodigal
[2024-01-24 15:19:50,513] [INFO] Running command: gunzip -c /var/lib/cwl/stg140395f5-3bf4-4272-b499-0526db7099a4/GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/cds.fna -a GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:05,459] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:05,460] [INFO] Task started: HMMsearch
[2024-01-24 15:20:05,460] [INFO] Running command: hmmsearch --tblout GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66feb33d-6f44-45f7-9dcb-604b7bac2d30/dqc_reference/reference_markers.hmm GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:05,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:05,870] [INFO] Found 6/6 markers.
[2024-01-24 15:20:05,934] [INFO] Query marker FASTA was written to GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:20:05,935] [INFO] Task started: Blastn
[2024-01-24 15:20:05,935] [INFO] Running command: blastn -query GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg66feb33d-6f44-45f7-9dcb-604b7bac2d30/dqc_reference/reference_markers.fasta -out GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:06,803] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:06,807] [INFO] Selected 14 target genomes.
[2024-01-24 15:20:06,808] [INFO] Target genome list was writen to GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:20:06,823] [INFO] Task started: fastANI
[2024-01-24 15:20:06,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg140395f5-3bf4-4272-b499-0526db7099a4/GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna.gz --refList GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:19,494] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:19,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66feb33d-6f44-45f7-9dcb-604b7bac2d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:19,495] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66feb33d-6f44-45f7-9dcb-604b7bac2d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:19,515] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:19,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:19,516] [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	97.8815	1580	1779	95	conclusive
Pseudomonas asuensis	strain=JCM 13501	GCA_014646755.1	1825787	1825787	type	True	85.388	1314	1779	95	below_threshold
Pseudomonas duriflava	strain=CGMCC 1.6858	GCA_007830155.1	459528	459528	type	True	79.4492	619	1779	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	78.0178	349	1779	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	77.9776	360	1779	95	below_threshold
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	77.9024	358	1779	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	77.8634	228	1779	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	77.8389	369	1779	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	77.7311	243	1779	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	77.6736	226	1779	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	77.6267	229	1779	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	77.5702	268	1779	95	below_threshold
Pseudomonas pohangensis	strain=DSM 17875	GCA_900105995.1	364197	364197	type	True	77.5522	169	1779	95	below_threshold
Serpens gallinarum	strain=Sa2CUA2	GCA_014836765.1	2763075	2763075	type	True	77.5115	193	1779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:19,518] [INFO] DFAST Taxonomy check result was written to GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:20:19,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:19,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:19,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66feb33d-6f44-45f7-9dcb-604b7bac2d30/dqc_reference/checkm_data
[2024-01-24 15:20:19,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:19,568] [INFO] Task started: CheckM
[2024-01-24 15:20:19,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/checkm_input GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:21:06,377] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:06,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:06,405] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:06,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:06,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:21:06,407] [INFO] Task started: Blastn
[2024-01-24 15:21:06,407] [INFO] Running command: blastn -query GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg66feb33d-6f44-45f7-9dcb-604b7bac2d30/dqc_reference/reference_markers_gtdb.fasta -out GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:07,823] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:07,827] [INFO] Selected 14 target genomes.
[2024-01-24 15:21:07,827] [INFO] Target genome list was writen to GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:07,839] [INFO] Task started: fastANI
[2024-01-24 15:21:07,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg140395f5-3bf4-4272-b499-0526db7099a4/GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna.gz --refList GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:21,403] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:21,422] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:21,422] [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	99.981	1730	1779	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	85.3838	1315	1779	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	79.4492	619	1779	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	78.1201	328	1779	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_001650425.1	s__Pseudomonas_B oryzihabitans_B	78.0368	345	1779	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	78.0018	342	1779	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_006384975.1	s__Pseudomonas_B psychrotolerans_B	77.9992	361	1779	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	77.9153	358	1779	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	77.6892	277	1779	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_009189165.1	s__Pseudomonas sp009189165	77.6357	273	1779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014836765.1	s__Pseudomonas_H sp014836765	77.5115	193	1779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	97.71	97.71	0.94	0.94	2	-
GCF_900112645.1	s__Pseudomonas_E straminea	77.4334	262	1779	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_900104805.1	s__Pseudomonas_K oryzae	77.35	218	1779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213805.1	s__Pseudomonas_E fulva_B	77.3125	257	1779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:21,439] [INFO] GTDB search result was written to GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:21,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:21,446] [INFO] DFAST_QC result json was written to GCF_900110795.1_IMG-taxon_2663762783_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:21:21,447] [INFO] DFAST_QC completed!
[2024-01-24 15:21:21,447] [INFO] Total running time: 0h1m32s