[2024-01-25 20:00:05,419] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:05,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:05,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e348153-56f5-4c6c-ac34-3dde66f02981/dqc_reference
[2024-01-25 20:00:06,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:06,511] [INFO] Task started: Prodigal
[2024-01-25 20:00:06,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f69a3fa-c65f-416d-b2e4-82be1b31040b/GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/cds.fna -a GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:28,954] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:28,954] [INFO] Task started: HMMsearch
[2024-01-25 20:00:28,954] [INFO] Running command: hmmsearch --tblout GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e348153-56f5-4c6c-ac34-3dde66f02981/dqc_reference/reference_markers.hmm GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:29,226] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:29,227] [INFO] Found 6/6 markers.
[2024-01-25 20:00:29,278] [INFO] Query marker FASTA was written to GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:00:29,278] [INFO] Task started: Blastn
[2024-01-25 20:00:29,278] [INFO] Running command: blastn -query GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e348153-56f5-4c6c-ac34-3dde66f02981/dqc_reference/reference_markers.fasta -out GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:30,145] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:30,147] [INFO] Selected 11 target genomes.
[2024-01-25 20:00:30,147] [INFO] Target genome list was writen to GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:00:30,156] [INFO] Task started: fastANI
[2024-01-25 20:00:30,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f69a3fa-c65f-416d-b2e4-82be1b31040b/GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna.gz --refList GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:50,566] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:50,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e348153-56f5-4c6c-ac34-3dde66f02981/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:50,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e348153-56f5-4c6c-ac34-3dde66f02981/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:50,574] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:00:50,575] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:50,575] [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 mandelii	strain=LMG 21607	GCA_900106065.1	75612	75612	suspected-type	True	100.0	2344	2347	95	conclusive
Pseudomonas mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	99.9767	2282	2347	95	conclusive
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	99.9495	2255	2347	95	conclusive
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	88.2804	1600	2347	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	88.243	1622	2347	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	86.6475	1528	2347	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	86.5284	1548	2347	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.0993	1539	2347	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.0684	1511	2347	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.5814	1558	2347	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	84.0003	1339	2347	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:50,577] [INFO] DFAST Taxonomy check result was written to GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:00:50,578] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:50,578] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:50,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e348153-56f5-4c6c-ac34-3dde66f02981/dqc_reference/checkm_data
[2024-01-25 20:00:50,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:50,646] [INFO] Task started: CheckM
[2024-01-25 20:00:50,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/checkm_input GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:01:55,380] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:55,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:55,398] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:55,398] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:55,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:01:55,399] [INFO] Task started: Blastn
[2024-01-25 20:01:55,399] [INFO] Running command: blastn -query GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e348153-56f5-4c6c-ac34-3dde66f02981/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:56,980] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:56,983] [INFO] Selected 13 target genomes.
[2024-01-25 20:01:56,983] [INFO] Target genome list was writen to GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:56,995] [INFO] Task started: fastANI
[2024-01-25 20:01:56,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f69a3fa-c65f-416d-b2e4-82be1b31040b/GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna.gz --refList GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:21,967] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:21,976] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:21,977] [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_900106065.1	s__Pseudomonas_E mandelii	100.0	2344	2347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.92	98.70	0.92	0.88	64	conclusive
GCF_003151075.1	s__Pseudomonas_E sp003151075	92.7255	1878	2347	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_004310295.1	s__Pseudomonas_E sp004310295	92.0385	1747	2347	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_900103875.1	s__Pseudomonas_E arsenicoxydans	89.4359	1733	2347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.47	96.47	0.86	0.86	2	-
GCF_000282315.2	s__Pseudomonas_E sp000282315	89.4133	1695	2347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.54	96.05	0.87	0.83	6	-
GCF_900187425.1	s__Pseudomonas_E sp900187425	89.4003	1698	2347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.77	95.75	0.84	0.83	4	-
GCF_000968015.1	s__Pseudomonas_E fluorescens_W	89.2988	1680	2347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
GCF_004136015.1	s__Pseudomonas_E sp004136015	89.2404	1693	2347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.14	95.84	0.91	0.90	3	-
GCF_018502625.1	s__Pseudomonas_E fluorescens_BW	88.8217	1677	2347	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_001297125.1	s__Pseudomonas_E sp001297125	88.7923	1666	2347	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_016650695.1	s__Pseudomonas_E sp016650695	88.071	1574	2347	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_006094435.1	s__Pseudomonas_E sp002029345	87.8659	1632	2347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.75	98.73	0.83	0.83	3	-
GCF_900105155.1	s__Pseudomonas_E prosekii	87.0581	1566	2347	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	96.34	0.92	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:21,986] [INFO] GTDB search result was written to GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:21,986] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:21,993] [INFO] DFAST_QC result json was written to GCF_900106065.1_IMG-taxon_2636416004_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:02:21,993] [INFO] DFAST_QC completed!
[2024-01-25 20:02:21,994] [INFO] Total running time: 0h2m17s