[2024-01-24 15:26:04,770] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:04,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:04,774] [INFO] DQC Reference Directory: /var/lib/cwl/stged860ec4-681c-4544-8f91-6f00887260b8/dqc_reference
[2024-01-24 15:26:07,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:07,024] [INFO] Task started: Prodigal
[2024-01-24 15:26:07,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f83a2f4-7979-4132-b330-39ca20984fd6/GCF_004217445.1_ASM421744v1_genomic.fna.gz | prodigal -d GCF_004217445.1_ASM421744v1_genomic.fna/cds.fna -a GCF_004217445.1_ASM421744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:18,870] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:18,871] [INFO] Task started: HMMsearch
[2024-01-24 15:26:18,871] [INFO] Running command: hmmsearch --tblout GCF_004217445.1_ASM421744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged860ec4-681c-4544-8f91-6f00887260b8/dqc_reference/reference_markers.hmm GCF_004217445.1_ASM421744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:19,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:19,155] [INFO] Found 6/6 markers.
[2024-01-24 15:26:19,190] [INFO] Query marker FASTA was written to GCF_004217445.1_ASM421744v1_genomic.fna/markers.fasta
[2024-01-24 15:26:19,191] [INFO] Task started: Blastn
[2024-01-24 15:26:19,191] [INFO] Running command: blastn -query GCF_004217445.1_ASM421744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged860ec4-681c-4544-8f91-6f00887260b8/dqc_reference/reference_markers.fasta -out GCF_004217445.1_ASM421744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:20,146] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:20,150] [INFO] Selected 30 target genomes.
[2024-01-24 15:26:20,151] [INFO] Target genome list was writen to GCF_004217445.1_ASM421744v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:20,164] [INFO] Task started: fastANI
[2024-01-24 15:26:20,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f83a2f4-7979-4132-b330-39ca20984fd6/GCF_004217445.1_ASM421744v1_genomic.fna.gz --refList GCF_004217445.1_ASM421744v1_genomic.fna/target_genomes.txt --output GCF_004217445.1_ASM421744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:26:40,709] [INFO] Task succeeded: fastANI
[2024-01-24 15:26:40,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged860ec4-681c-4544-8f91-6f00887260b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:26:40,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged860ec4-681c-4544-8f91-6f00887260b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:26:40,740] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:26:40,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:26:40,740] [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
Fluviicoccus keumensis	strain=DSM 105135	GCA_004217445.1	1435465	1435465	type	True	100.0	1218	1219	95	conclusive
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	77.7395	164	1219	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.7336	206	1219	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	77.7169	234	1219	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	77.6755	237	1219	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	77.6276	115	1219	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	77.6152	206	1219	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	77.6071	210	1219	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	77.5516	179	1219	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	77.5412	195	1219	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	77.5285	213	1219	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	77.4818	116	1219	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	77.4253	200	1219	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	77.4019	153	1219	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	77.3898	155	1219	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.3609	176	1219	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	77.2681	134	1219	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	77.1802	153	1219	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	77.146	156	1219	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	77.0541	163	1219	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	77.0526	132	1219	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	76.989	118	1219	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	76.96	95	1219	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	76.8068	130	1219	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	76.6902	159	1219	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.6707	105	1219	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.6207	106	1219	95	below_threshold
Cupriavidus gilardii	strain=CCUG 38401	GCA_008801915.1	82541	82541	type	True	76.533	123	1219	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.5225	101	1219	95	below_threshold
Cupriavidus gilardii	strain=ATCC 700815	GCA_013004615.1	82541	82541	type	True	76.4635	124	1219	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:26:40,743] [INFO] DFAST Taxonomy check result was written to GCF_004217445.1_ASM421744v1_genomic.fna/tc_result.tsv
[2024-01-24 15:26:40,743] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:26:40,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:26:40,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged860ec4-681c-4544-8f91-6f00887260b8/dqc_reference/checkm_data
[2024-01-24 15:26:40,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:26:40,784] [INFO] Task started: CheckM
[2024-01-24 15:26:40,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217445.1_ASM421744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217445.1_ASM421744v1_genomic.fna/checkm_input GCF_004217445.1_ASM421744v1_genomic.fna/checkm_result
[2024-01-24 15:27:18,948] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:18,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:18,977] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:18,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:18,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217445.1_ASM421744v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:18,979] [INFO] Task started: Blastn
[2024-01-24 15:27:18,979] [INFO] Running command: blastn -query GCF_004217445.1_ASM421744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged860ec4-681c-4544-8f91-6f00887260b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217445.1_ASM421744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:20,704] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:20,709] [INFO] Selected 26 target genomes.
[2024-01-24 15:27:20,709] [INFO] Target genome list was writen to GCF_004217445.1_ASM421744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:20,751] [INFO] Task started: fastANI
[2024-01-24 15:27:20,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f83a2f4-7979-4132-b330-39ca20984fd6/GCF_004217445.1_ASM421744v1_genomic.fna.gz --refList GCF_004217445.1_ASM421744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217445.1_ASM421744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:38,490] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:38,513] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:38,514] [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_004217445.1	s__Fluviicoccus keumensis	100.0	1218	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Fluviicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002943415.1	s__Perlucidibaca sp002943415	79.6012	207	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420045.1	s__Perlucidibaca piscinae	78.7045	238	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Perlucidibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877905.1	s__Pseudomonas nicosulfuronedens	77.9284	187	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187975.1	s__Pseudomonas delhiensis	77.7325	233	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCA_018262975.1	s__JADFDG01 sp018262975	77.7078	208	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__JADFDG01;g__JADFDG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	77.6514	200	1219	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_000467105.1	s__Pseudomonas_E alcaligenes	77.63	205	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_900100495.1	s__Pseudomonas_E benzenivorans	77.5021	214	1219	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	77.4932	218	1219	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_013409135.1	s__Pseudomonas_A kunmingensis_A	77.4803	127	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	77.3172	145	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_015265435.1	s__Alcanivorax profundimaris	77.1672	154	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_900112645.1	s__Pseudomonas_E straminea	77.1314	177	1219	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_005938655.1	s__Alcanivorax gelatiniphagus	77.0543	163	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_002864685.1	s__Alcanivorax mobilis	77.0099	117	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	-
GCF_905120355.1	s__Azonexus sp012839675	76.9868	67	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.59	97.59	0.83	0.83	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	76.9834	94	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018826895.1	s__Pseudomonas_E sp018826895	76.8054	107	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.86	99.82	0.88	0.84	6	-
GCF_900094595.1	s__Cupriavidus alkaliphilus	76.6908	158	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	96.96	96.04	0.91	0.89	16	-
GCA_002389055.1	s__Alcanivorax sp002389055	76.6852	128	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.98	96.27	0.78	0.74	3	-
GCF_003865015.1	s__Sulfurisoma sediminicola	76.6001	107	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	76.5791	104	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900250115.1	s__Cupriavidus taiwanensis_B	76.3913	169	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.46	95.70	0.97	0.87	14	-
GCF_013314895.1	s__Cupriavidus gilardii_C	76.3826	128	1219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	95.09	95.09	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:38,517] [INFO] GTDB search result was written to GCF_004217445.1_ASM421744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:38,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:38,523] [INFO] DFAST_QC result json was written to GCF_004217445.1_ASM421744v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:38,523] [INFO] DFAST_QC completed!
[2024-01-24 15:27:38,523] [INFO] Total running time: 0h1m34s