[2024-01-25 18:01:36,273] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:01:36,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:01:36,275] [INFO] DQC Reference Directory: /var/lib/cwl/stge44874bb-dd3a-476b-981e-32992965d3d5/dqc_reference
[2024-01-25 18:01:37,430] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:01:37,433] [INFO] Task started: Prodigal
[2024-01-25 18:01:37,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e4a0561-a746-49fd-99ec-db42113f2144/GCF_003595175.1_ASM359517v1_genomic.fna.gz | prodigal -d GCF_003595175.1_ASM359517v1_genomic.fna/cds.fna -a GCF_003595175.1_ASM359517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:01:50,843] [INFO] Task succeeded: Prodigal
[2024-01-25 18:01:50,843] [INFO] Task started: HMMsearch
[2024-01-25 18:01:50,843] [INFO] Running command: hmmsearch --tblout GCF_003595175.1_ASM359517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge44874bb-dd3a-476b-981e-32992965d3d5/dqc_reference/reference_markers.hmm GCF_003595175.1_ASM359517v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:01:51,075] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:01:51,076] [INFO] Found 6/6 markers.
[2024-01-25 18:01:51,115] [INFO] Query marker FASTA was written to GCF_003595175.1_ASM359517v1_genomic.fna/markers.fasta
[2024-01-25 18:01:51,115] [INFO] Task started: Blastn
[2024-01-25 18:01:51,115] [INFO] Running command: blastn -query GCF_003595175.1_ASM359517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge44874bb-dd3a-476b-981e-32992965d3d5/dqc_reference/reference_markers.fasta -out GCF_003595175.1_ASM359517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:52,043] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:52,046] [INFO] Selected 18 target genomes.
[2024-01-25 18:01:52,046] [INFO] Target genome list was writen to GCF_003595175.1_ASM359517v1_genomic.fna/target_genomes.txt
[2024-01-25 18:01:52,058] [INFO] Task started: fastANI
[2024-01-25 18:01:52,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4a0561-a746-49fd-99ec-db42113f2144/GCF_003595175.1_ASM359517v1_genomic.fna.gz --refList GCF_003595175.1_ASM359517v1_genomic.fna/target_genomes.txt --output GCF_003595175.1_ASM359517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:15,247] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:15,248] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge44874bb-dd3a-476b-981e-32992965d3d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:15,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge44874bb-dd3a-476b-981e-32992965d3d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:15,260] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:15,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:15,260] [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 cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	100.0	1648	1649	95	conclusive
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	85.9423	1105	1649	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	85.7734	1147	1649	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.2542	950	1649	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	84.1866	1042	1649	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	83.6687	936	1649	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	83.654	1065	1649	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	83.6341	927	1649	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	83.6006	921	1649	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	83.3496	912	1649	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	83.3381	955	1649	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	83.2686	1035	1649	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	82.8089	797	1649	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	82.7304	822	1649	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.5758	788	1649	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	82.2094	863	1649	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	82.1923	839	1649	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.6788	728	1649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:15,261] [INFO] DFAST Taxonomy check result was written to GCF_003595175.1_ASM359517v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:15,263] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:15,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:15,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge44874bb-dd3a-476b-981e-32992965d3d5/dqc_reference/checkm_data
[2024-01-25 18:02:15,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:15,313] [INFO] Task started: CheckM
[2024-01-25 18:02:15,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003595175.1_ASM359517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003595175.1_ASM359517v1_genomic.fna/checkm_input GCF_003595175.1_ASM359517v1_genomic.fna/checkm_result
[2024-01-25 18:02:54,628] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:54,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:54,646] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:54,646] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:54,646] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003595175.1_ASM359517v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:54,646] [INFO] Task started: Blastn
[2024-01-25 18:02:54,646] [INFO] Running command: blastn -query GCF_003595175.1_ASM359517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge44874bb-dd3a-476b-981e-32992965d3d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003595175.1_ASM359517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:56,473] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:56,477] [INFO] Selected 17 target genomes.
[2024-01-25 18:02:56,478] [INFO] Target genome list was writen to GCF_003595175.1_ASM359517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:56,495] [INFO] Task started: fastANI
[2024-01-25 18:02:56,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e4a0561-a746-49fd-99ec-db42113f2144/GCF_003595175.1_ASM359517v1_genomic.fna.gz --refList GCF_003595175.1_ASM359517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003595175.1_ASM359517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:18,575] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:18,585] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:18,586] [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_003595175.1	s__Pseudomonas_E sp003595175	100.0	1648	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_904061905.1	s__Pseudomonas_E carbonaria	85.9346	1106	1649	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_016901015.1	s__Pseudomonas_E sp016901015	85.7835	1146	1649	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_009799925.1	s__Pseudomonas_E sp009799925	84.6646	960	1649	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_902506505.1	s__Pseudomonas_E sp902506505	84.411	979	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	84.2596	954	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	84.2061	1040	1649	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_013200955.2	s__Pseudomonas_E campi	83.5867	915	1649	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_014851905.1	s__Pseudomonas_E sp014851905	83.3685	910	1649	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_014174475.1	s__Pseudomonas_E sp014174475	83.3568	954	1649	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_900112375.1	s__Pseudomonas citronellolis	83.2404	1060	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	82.7205	826	1649	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_019097855.1	s__Pseudomonas_K sp019097855	82.5592	790	1649	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_002890915.1	s__Pseudomonas_A stutzeri_AF	82.333	776	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_900636545.1	s__Pseudomonas_E mendocina	82.2463	862	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	97.19	0.93	0.89	14	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	81.9725	762	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_002304225.1	s__Pseudomonas_E sp002304225	81.9602	739	1649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.09	95.09	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:18,587] [INFO] GTDB search result was written to GCF_003595175.1_ASM359517v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:18,588] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:18,593] [INFO] DFAST_QC result json was written to GCF_003595175.1_ASM359517v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:18,593] [INFO] DFAST_QC completed!
[2024-01-25 18:03:18,593] [INFO] Total running time: 0h1m42s