[2024-01-24 13:49:40,816] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,818] [INFO] DQC Reference Directory: /var/lib/cwl/stgb34535f6-b6d3-41dc-9932-531830a8e0e2/dqc_reference
[2024-01-24 13:49:42,185] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,186] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,186] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2748023-275c-46f0-bfab-44c67b15099a/GCF_005876855.1_ASM587685v1_genomic.fna.gz | prodigal -d GCF_005876855.1_ASM587685v1_genomic.fna/cds.fna -a GCF_005876855.1_ASM587685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:56,274] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:56,274] [INFO] Task started: HMMsearch
[2024-01-24 13:49:56,274] [INFO] Running command: hmmsearch --tblout GCF_005876855.1_ASM587685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb34535f6-b6d3-41dc-9932-531830a8e0e2/dqc_reference/reference_markers.hmm GCF_005876855.1_ASM587685v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:56,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:56,685] [INFO] Found 6/6 markers.
[2024-01-24 13:49:56,753] [INFO] Query marker FASTA was written to GCF_005876855.1_ASM587685v1_genomic.fna/markers.fasta
[2024-01-24 13:49:56,753] [INFO] Task started: Blastn
[2024-01-24 13:49:56,754] [INFO] Running command: blastn -query GCF_005876855.1_ASM587685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34535f6-b6d3-41dc-9932-531830a8e0e2/dqc_reference/reference_markers.fasta -out GCF_005876855.1_ASM587685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,865] [INFO] Selected 29 target genomes.
[2024-01-24 13:49:57,866] [INFO] Target genome list was writen to GCF_005876855.1_ASM587685v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:57,874] [INFO] Task started: fastANI
[2024-01-24 13:49:57,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2748023-275c-46f0-bfab-44c67b15099a/GCF_005876855.1_ASM587685v1_genomic.fna.gz --refList GCF_005876855.1_ASM587685v1_genomic.fna/target_genomes.txt --output GCF_005876855.1_ASM587685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:26,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:26,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb34535f6-b6d3-41dc-9932-531830a8e0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:26,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb34535f6-b6d3-41dc-9932-531830a8e0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:26,371] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:26,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:26,372] [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] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	100.0	1540	1544	95	conclusive
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	84.1498	1011	1544	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	82.7965	864	1544	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	82.7955	856	1544	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	82.7883	927	1544	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	82.7759	852	1544	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	82.7562	924	1544	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	82.6788	946	1544	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.4213	795	1544	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	82.101	812	1544	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	81.7794	774	1544	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	81.7668	764	1544	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	81.7612	784	1544	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.618	617	1544	95	below_threshold
[Pseudomonas] urumqiensis	strain=T3	GCA_003640395.1	638269	638269	type	True	81.5989	865	1544	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.397	773	1544	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	81.3745	725	1544	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.3615	729	1544	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	81.2108	624	1544	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	81.0679	687	1544	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	80.4324	758	1544	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	80.4166	753	1544	95	below_threshold
Serpens gallinarum	strain=Sa2CUA2	GCA_014836765.1	2763075	2763075	type	True	79.8611	587	1544	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	78.862	595	1544	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	78.8185	585	1544	95	below_threshold
Pseudomonas paraversuta	strain=V4/DAB/S4/2a	GCA_904063065.1	2750624	2750624	type	True	78.3544	416	1544	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	77.2434	280	1544	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	76.5486	138	1544	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.1899	213	1544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,377] [INFO] DFAST Taxonomy check result was written to GCF_005876855.1_ASM587685v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:26,378] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:26,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:26,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb34535f6-b6d3-41dc-9932-531830a8e0e2/dqc_reference/checkm_data
[2024-01-24 13:50:26,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:26,431] [INFO] Task started: CheckM
[2024-01-24 13:50:26,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005876855.1_ASM587685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005876855.1_ASM587685v1_genomic.fna/checkm_input GCF_005876855.1_ASM587685v1_genomic.fna/checkm_result
[2024-01-24 13:51:09,145] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:09,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:09,167] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:09,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:09,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005876855.1_ASM587685v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:09,169] [INFO] Task started: Blastn
[2024-01-24 13:51:09,169] [INFO] Running command: blastn -query GCF_005876855.1_ASM587685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34535f6-b6d3-41dc-9932-531830a8e0e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_005876855.1_ASM587685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:10,911] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:10,916] [INFO] Selected 20 target genomes.
[2024-01-24 13:51:10,917] [INFO] Target genome list was writen to GCF_005876855.1_ASM587685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:10,981] [INFO] Task started: fastANI
[2024-01-24 13:51:10,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2748023-275c-46f0-bfab-44c67b15099a/GCF_005876855.1_ASM587685v1_genomic.fna.gz --refList GCF_005876855.1_ASM587685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005876855.1_ASM587685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:31,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:31,490] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:31,490] [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_005876855.1	s__Pseudomonas_R nosocomialis	100.0	1540	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	conclusive
GCA_900766265.1	s__Pseudomonas_R sp900766265	92.6917	1244	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013522725.1	s__Pseudomonas_R azotifigens_A	91.4409	1329	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	84.1456	1012	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	83.5542	956	1544	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_015070855.1	s__Pseudomonas_A lopnurensis	83.3253	940	1544	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_000263395.1	s__Pseudomonas_A stutzeri_C	83.0686	830	1544	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_003696285.1	s__Pseudomonas_A nitrititolerans	82.4519	877	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.45	96.83	0.90	0.83	53	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	82.4218	795	1544	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_900106975.1	s__Pseudomonas_O kuykendallii	81.8082	780	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	96.83	96.68	0.93	0.91	4	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	81.3271	843	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_003052585.1	s__Pseudomonas_E mangrovi	81.0396	690	1544	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_000952685.1	s__Pseudomonas_A stutzeri_E	80.8157	864	1544	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_013523125.1	s__Pseudomonas_E entomophila_B	80.3021	622	1544	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_000425785.1	s__Pseudomonas_E taiwanensis	79.814	612	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.59	99.45	0.93	0.87	8	-
GCF_012935755.1	s__Pseudomonas_E sp012935755	78.9983	604	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002723575.1	s__Pseudomonas_E viridiflava_B	78.7918	544	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.78	98.76	0.95	0.94	5	-
GCF_004803755.1	s__Pseudomonas_E sp004803755	78.4353	477	1544	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_000364845.1	s__Marinobacter_A nanhaiticus	76.5486	138	1544	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_018820665.1	s__Brevundimonas sp018820665	75.4298	85	1544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.88	99.88	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:31,492] [INFO] GTDB search result was written to GCF_005876855.1_ASM587685v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:31,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:31,499] [INFO] DFAST_QC result json was written to GCF_005876855.1_ASM587685v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:31,499] [INFO] DFAST_QC completed!
[2024-01-24 13:51:31,499] [INFO] Total running time: 0h1m51s