[2024-01-24 15:10:23,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:23,070] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:23,070] [INFO] DQC Reference Directory: /var/lib/cwl/stg17dff7b4-a9dc-4a6c-a1b9-9b5f1297bb8f/dqc_reference
[2024-01-24 15:10:24,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,571] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg06ddc8c9-fb40-422a-bd78-5089bc1db602/GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/cds.fna -a GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:36,199] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:36,199] [INFO] Task started: HMMsearch
[2024-01-24 15:10:36,199] [INFO] Running command: hmmsearch --tblout GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17dff7b4-a9dc-4a6c-a1b9-9b5f1297bb8f/dqc_reference/reference_markers.hmm GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:36,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:36,449] [INFO] Found 6/6 markers.
[2024-01-24 15:10:36,478] [INFO] Query marker FASTA was written to GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:10:36,479] [INFO] Task started: Blastn
[2024-01-24 15:10:36,479] [INFO] Running command: blastn -query GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg17dff7b4-a9dc-4a6c-a1b9-9b5f1297bb8f/dqc_reference/reference_markers.fasta -out GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:37,418] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:37,421] [INFO] Selected 29 target genomes.
[2024-01-24 15:10:37,421] [INFO] Target genome list was writen to GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:10:37,431] [INFO] Task started: fastANI
[2024-01-24 15:10:37,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ddc8c9-fb40-422a-bd78-5089bc1db602/GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna.gz --refList GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:03,461] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:03,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17dff7b4-a9dc-4a6c-a1b9-9b5f1297bb8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:03,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17dff7b4-a9dc-4a6c-a1b9-9b5f1297bb8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:03,485] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:03,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:03,485] [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
Atopomonas hussainii	strain=JCM 19513	GCA_900109735.1	1429083	1429083	type	True	100.0	1201	1203	95	conclusive
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	78.6788	370	1203	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.6492	343	1203	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	78.6334	351	1203	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	78.6199	409	1203	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.531	420	1203	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	78.5274	398	1203	95	below_threshold
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	78.4635	368	1203	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	78.462	405	1203	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	78.4554	343	1203	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	78.4427	423	1203	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	78.4081	422	1203	95	below_threshold
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	78.3898	377	1203	95	below_threshold
Pseudomonas nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	78.3764	390	1203	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	78.3467	352	1203	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.3303	407	1203	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	78.3144	352	1203	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	78.1348	313	1203	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	78.0981	318	1203	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	78.0069	324	1203	95	below_threshold
Pseudomonas vranovensis	strain=DSM 16006	GCA_000425805.1	321661	321661	type	True	77.8772	299	1203	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	77.8695	234	1203	95	below_threshold
Pseudomonas pisciculturae	strain=P115	GCA_015461805.1	2730413	2730413	type	True	77.8434	293	1203	95	below_threshold
Pseudomonas tolaasii		GCA_900625075.1	29442	29442	type	True	77.8364	313	1203	95	below_threshold
Pseudomonas tolaasii	strain=NCPPB 2192	GCA_002813445.1	29442	29442	type	True	77.8267	314	1203	95	below_threshold
Pseudomonas tolaasii	strain=CCUG 23369	GCA_008801395.1	29442	29442	type	True	77.8205	319	1203	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	77.8089	237	1203	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	77.73	278	1203	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	77.709	272	1203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:03,487] [INFO] DFAST Taxonomy check result was written to GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:11:03,487] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:03,487] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:03,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17dff7b4-a9dc-4a6c-a1b9-9b5f1297bb8f/dqc_reference/checkm_data
[2024-01-24 15:11:03,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:03,528] [INFO] Task started: CheckM
[2024-01-24 15:11:03,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/checkm_input GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:11:40,636] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:40,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:40,679] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:40,679] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:40,680] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:11:40,680] [INFO] Task started: Blastn
[2024-01-24 15:11:40,680] [INFO] Running command: blastn -query GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg17dff7b4-a9dc-4a6c-a1b9-9b5f1297bb8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:42,382] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:42,390] [INFO] Selected 27 target genomes.
[2024-01-24 15:11:42,390] [INFO] Target genome list was writen to GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:42,431] [INFO] Task started: fastANI
[2024-01-24 15:11:42,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg06ddc8c9-fb40-422a-bd78-5089bc1db602/GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna.gz --refList GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:06,652] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:06,674] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:06,675] [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_900109735.1	s__Pseudomonas_L hussainii	100.0	1201	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_L	95.0	95.93	95.93	0.92	0.92	2	conclusive
GCF_001592875.1	s__Pseudomonas_E sp001592875	78.9802	401	1203	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_014490745.1	s__Pseudomonas_E alcaligenes_C	78.959	436	1203	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_000761545.1	s__Pseudomonas_E sp000761545	78.8019	417	1203	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_008041835.1	s__Pseudomonas_E sp002282595	78.739	386	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_014851565.1	s__Pseudomonas_E sp014851565	78.6803	418	1203	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_016008875.1	s__Pseudomonas_E sp002439135	78.4936	404	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
GCF_900103845.1	s__Pseudomonas jinjuensis	78.4506	408	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900187975.1	s__Pseudomonas delhiensis	78.4457	424	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_017491605.1	s__Pseudomonas sp017491605	78.4037	389	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949385.2	s__Pseudomonas_F sp000949385	78.3956	369	1203	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_000213805.1	s__Pseudomonas_E fulva_B	78.3764	354	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_016919445.1	s__Pseudomonas sp016919445	78.3575	394	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708505.1	s__Pseudomonas_F sp001708505	78.347	374	1203	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_000423545.1	s__Pseudomonas_F resinovorans	78.3419	340	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.91	98.91	0.88	0.88	2	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	78.3391	406	1203	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_003052585.1	s__Pseudomonas_E mangrovi	78.3356	352	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	78.2679	352	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001446935.1	s__Pseudomonas_E sp001446935	78.2262	278	1203	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_002806685.1	s__Pseudomonas_E qingdaonensis	78.1526	343	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	78.1019	317	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_000259195.1	s__Pseudomonas_E donghuensis	78.0452	337	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.33	99.30	0.94	0.92	5	-
GCF_003097075.1	s__Pseudomonas_E sp003097075	77.9518	345	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_000425805.1	s__Pseudomonas_E vranovensis	77.8701	299	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.71	99.71	0.93	0.93	2	-
GCF_013385965.1	s__Pseudomonas_E edaphica	77.8349	324	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.93	0.94	0.92	9	-
GCF_002813445.1	s__Pseudomonas_E tolaasii	77.8335	314	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.61	99.17	0.97	0.93	14	-
GCF_000293885.2	s__Pseudomonas_E fluorescens_B	77.8149	312	1203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:06,677] [INFO] GTDB search result was written to GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:06,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:06,684] [INFO] DFAST_QC result json was written to GCF_900109735.1_IMG-taxon_2663763602_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:12:06,684] [INFO] DFAST_QC completed!
[2024-01-24 15:12:06,684] [INFO] Total running time: 0h1m44s