[2024-01-24 14:15:02,701] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e6e58c2-a907-4d69-8c07-4a69d2acdbb1/dqc_reference
[2024-01-24 14:15:04,187] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:04,188] [INFO] Task started: Prodigal
[2024-01-24 14:15:04,188] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e426a62-e005-4139-9d5f-f448f30cde9c/GCF_014647635.1_ASM1464763v1_genomic.fna.gz | prodigal -d GCF_014647635.1_ASM1464763v1_genomic.fna/cds.fna -a GCF_014647635.1_ASM1464763v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:19,950] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:19,950] [INFO] Task started: HMMsearch
[2024-01-24 14:15:19,950] [INFO] Running command: hmmsearch --tblout GCF_014647635.1_ASM1464763v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e6e58c2-a907-4d69-8c07-4a69d2acdbb1/dqc_reference/reference_markers.hmm GCF_014647635.1_ASM1464763v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:20,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:20,267] [INFO] Found 6/6 markers.
[2024-01-24 14:15:20,309] [INFO] Query marker FASTA was written to GCF_014647635.1_ASM1464763v1_genomic.fna/markers.fasta
[2024-01-24 14:15:20,310] [INFO] Task started: Blastn
[2024-01-24 14:15:20,310] [INFO] Running command: blastn -query GCF_014647635.1_ASM1464763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6e58c2-a907-4d69-8c07-4a69d2acdbb1/dqc_reference/reference_markers.fasta -out GCF_014647635.1_ASM1464763v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:21,216] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:21,219] [INFO] Selected 29 target genomes.
[2024-01-24 14:15:21,219] [INFO] Target genome list was writen to GCF_014647635.1_ASM1464763v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:21,243] [INFO] Task started: fastANI
[2024-01-24 14:15:21,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e426a62-e005-4139-9d5f-f448f30cde9c/GCF_014647635.1_ASM1464763v1_genomic.fna.gz --refList GCF_014647635.1_ASM1464763v1_genomic.fna/target_genomes.txt --output GCF_014647635.1_ASM1464763v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:44,526] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:44,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e6e58c2-a907-4d69-8c07-4a69d2acdbb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:44,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e6e58c2-a907-4d69-8c07-4a69d2acdbb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:44,548] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:44,548] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:44,548] [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 matsuisoli	strain=JCM 30078	GCA_014647635.1	1515666	1515666	type	True	100.0	1527	1527	95	conclusive
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	78.7153	381	1527	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	78.6326	386	1527	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	78.6147	365	1527	95	below_threshold
Pseudomonas oleovorans	strain=NCTC10692	GCA_900455615.1	301	301	type	True	78.6119	371	1527	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.5896	343	1527	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	78.5871	330	1527	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	78.5845	301	1527	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	78.5762	337	1527	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	78.5717	332	1527	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	78.5655	329	1527	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	78.5526	405	1527	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	78.5463	322	1527	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	78.546	443	1527	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	78.5429	299	1527	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	78.5245	381	1527	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	78.5244	334	1527	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	78.5144	379	1527	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	78.4997	363	1527	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	78.4966	320	1527	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	78.4945	373	1527	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	78.4555	364	1527	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	78.4401	386	1527	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	78.318	333	1527	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	78.3101	415	1527	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	78.2872	420	1527	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	78.2805	331	1527	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	78.2469	340	1527	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	77.9587	309	1527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:44,550] [INFO] DFAST Taxonomy check result was written to GCF_014647635.1_ASM1464763v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:44,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:44,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:44,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e6e58c2-a907-4d69-8c07-4a69d2acdbb1/dqc_reference/checkm_data
[2024-01-24 14:15:44,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:44,594] [INFO] Task started: CheckM
[2024-01-24 14:15:44,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647635.1_ASM1464763v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647635.1_ASM1464763v1_genomic.fna/checkm_input GCF_014647635.1_ASM1464763v1_genomic.fna/checkm_result
[2024-01-24 14:16:30,789] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:30,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:30,812] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:30,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:30,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647635.1_ASM1464763v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:30,814] [INFO] Task started: Blastn
[2024-01-24 14:16:30,814] [INFO] Running command: blastn -query GCF_014647635.1_ASM1464763v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6e58c2-a907-4d69-8c07-4a69d2acdbb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647635.1_ASM1464763v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:32,350] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:32,355] [INFO] Selected 29 target genomes.
[2024-01-24 14:16:32,355] [INFO] Target genome list was writen to GCF_014647635.1_ASM1464763v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:32,377] [INFO] Task started: fastANI
[2024-01-24 14:16:32,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e426a62-e005-4139-9d5f-f448f30cde9c/GCF_014647635.1_ASM1464763v1_genomic.fna.gz --refList GCF_014647635.1_ASM1464763v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647635.1_ASM1464763v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:58,706] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:58,731] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:58,732] [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_014647635.1	s__Pseudomonas_P matsuisoli	100.0	1527	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_P	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	78.862	341	1527	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_004521985.1	s__Pseudomonas_E khazarica	78.7688	411	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	78.7267	318	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	78.7086	354	1527	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	78.6771	343	1527	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_000412695.1	s__Pseudomonas_F resinovorans_A	78.6325	396	1527	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_907163115.1	s__Pseudomonas_A stutzeri_AL	78.621	323	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
GCF_002355475.1	s__Pseudomonas_F furukawaii	78.6182	388	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	99.26	98.53	0.90	0.84	3	-
GCF_902506505.1	s__Pseudomonas_E sp902506505	78.6054	357	1527	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_000219605.1	s__Pseudomonas_A stutzeri	78.591	327	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003595175.1	s__Pseudomonas_E sp003595175	78.5774	344	1527	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_012767755.2	s__Pseudomonas_F sp003234055	78.5428	406	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
GCF_001839655.1	s__Pseudomonas_E argentinensis_B	78.5285	420	1527	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	78.5126	408	1527	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_002091755.1	s__Pseudomonas nitroreducens	78.5015	373	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.47	95.19	0.93	0.83	16	-
GCF_014164785.1	s__Pseudomonas_E sp014164785	78.4966	320	1527	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_001945445.1	s__Pseudomonas_E sp001945445	78.4754	408	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.91	0.91	2	-
GCF_014174475.1	s__Pseudomonas_E sp014174475	78.4719	362	1527	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_004327285.1	s__Pseudomonas_E daroniae	78.4658	415	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	98.61	0.97	0.93	4	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	78.4533	327	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	78.4428	385	1527	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_000327065.1	s__Pseudomonas_A stutzeri_AE	78.414	328	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	78.3398	403	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013522825.1	s__Pseudomonas_A stutzeri_AK	78.3193	337	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495915.1	s__Pseudomonas_A chloritidismutans	78.298	333	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCF_002890795.1	s__Pseudomonas_A stutzeri_AA	78.2871	302	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919445.1	s__Pseudomonas sp016919445	78.2627	399	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002476945.1	s__Pseudomonas_A stutzeri_Q	77.898	273	1527	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:58,733] [INFO] GTDB search result was written to GCF_014647635.1_ASM1464763v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:58,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:58,740] [INFO] DFAST_QC result json was written to GCF_014647635.1_ASM1464763v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:58,741] [INFO] DFAST_QC completed!
[2024-01-24 14:16:58,741] [INFO] Total running time: 0h1m56s