[2024-01-25 18:16:50,579] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:50,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:50,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eb0b0bc-9f84-4704-8261-aec9ec90c705/dqc_reference
[2024-01-25 18:16:51,701] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:51,702] [INFO] Task started: Prodigal
[2024-01-25 18:16:51,702] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2d51c77-e4d8-4600-bc9e-297d88822bc4/GCF_022601735.1_ASM2260173v1_genomic.fna.gz | prodigal -d GCF_022601735.1_ASM2260173v1_genomic.fna/cds.fna -a GCF_022601735.1_ASM2260173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:17:02,157] [INFO] Task succeeded: Prodigal
[2024-01-25 18:17:02,157] [INFO] Task started: HMMsearch
[2024-01-25 18:17:02,158] [INFO] Running command: hmmsearch --tblout GCF_022601735.1_ASM2260173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eb0b0bc-9f84-4704-8261-aec9ec90c705/dqc_reference/reference_markers.hmm GCF_022601735.1_ASM2260173v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:02,366] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:02,367] [INFO] Found 6/6 markers.
[2024-01-25 18:17:02,396] [INFO] Query marker FASTA was written to GCF_022601735.1_ASM2260173v1_genomic.fna/markers.fasta
[2024-01-25 18:17:02,396] [INFO] Task started: Blastn
[2024-01-25 18:17:02,396] [INFO] Running command: blastn -query GCF_022601735.1_ASM2260173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eb0b0bc-9f84-4704-8261-aec9ec90c705/dqc_reference/reference_markers.fasta -out GCF_022601735.1_ASM2260173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:03,228] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:03,231] [INFO] Selected 29 target genomes.
[2024-01-25 18:17:03,231] [INFO] Target genome list was writen to GCF_022601735.1_ASM2260173v1_genomic.fna/target_genomes.txt
[2024-01-25 18:17:03,243] [INFO] Task started: fastANI
[2024-01-25 18:17:03,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2d51c77-e4d8-4600-bc9e-297d88822bc4/GCF_022601735.1_ASM2260173v1_genomic.fna.gz --refList GCF_022601735.1_ASM2260173v1_genomic.fna/target_genomes.txt --output GCF_022601735.1_ASM2260173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:26,916] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:26,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eb0b0bc-9f84-4704-8261-aec9ec90c705/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:26,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eb0b0bc-9f84-4704-8261-aec9ec90c705/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:26,933] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:17:26,933] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:17:26,933] [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	82.2456	847	1175	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	78.5266	310	1175	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	78.4341	313	1175	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_900102635.1	489632	489632	type	True	78.3961	320	1175	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	78.3019	322	1175	95	below_threshold
Pseudomonas fluvialis	strain=CCM 8778	GCA_014635625.1	1793966	1793966	suspected-type	True	78.2931	275	1175	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	78.2775	221	1175	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	78.2771	313	1175	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	78.1704	352	1175	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.1647	241	1175	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	78.148	285	1175	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	78.1314	318	1175	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	78.0983	291	1175	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	78.075	218	1175	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	78.0721	322	1175	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	78.0634	352	1175	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	78.0595	353	1175	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	78.0193	223	1175	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	77.9798	307	1175	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	77.978	278	1175	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	77.9418	269	1175	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	77.884	268	1175	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	77.8671	317	1175	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	77.7412	265	1175	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	77.7291	228	1175	95	below_threshold
Pseudomonas asgharzadehiana	strain=SWRI132	GCA_019139815.1	2842349	2842349	type	True	77.6293	216	1175	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	77.5457	206	1175	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	77.3844	235	1175	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	77.3293	242	1175	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:26,935] [INFO] DFAST Taxonomy check result was written to GCF_022601735.1_ASM2260173v1_genomic.fna/tc_result.tsv
[2024-01-25 18:17:26,935] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:26,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:26,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eb0b0bc-9f84-4704-8261-aec9ec90c705/dqc_reference/checkm_data
[2024-01-25 18:17:26,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:26,974] [INFO] Task started: CheckM
[2024-01-25 18:17:26,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022601735.1_ASM2260173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022601735.1_ASM2260173v1_genomic.fna/checkm_input GCF_022601735.1_ASM2260173v1_genomic.fna/checkm_result
[2024-01-25 18:17:59,168] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:59,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:59,185] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:59,185] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:59,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022601735.1_ASM2260173v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:59,186] [INFO] Task started: Blastn
[2024-01-25 18:17:59,186] [INFO] Running command: blastn -query GCF_022601735.1_ASM2260173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eb0b0bc-9f84-4704-8261-aec9ec90c705/dqc_reference/reference_markers_gtdb.fasta -out GCF_022601735.1_ASM2260173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:18:00,612] [INFO] Task succeeded: Blastn
[2024-01-25 18:18:00,615] [INFO] Selected 28 target genomes.
[2024-01-25 18:18:00,615] [INFO] Target genome list was writen to GCF_022601735.1_ASM2260173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:18:00,642] [INFO] Task started: fastANI
[2024-01-25 18:18:00,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2d51c77-e4d8-4600-bc9e-297d88822bc4/GCF_022601735.1_ASM2260173v1_genomic.fna.gz --refList GCF_022601735.1_ASM2260173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022601735.1_ASM2260173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:24,330] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:24,351] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:18:24,352] [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	82.2594	846	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_L	95.0	95.93	95.93	0.92	0.92	2	-
GCF_008041835.1	s__Pseudomonas_E sp002282595	78.5392	306	1175	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_001941865.1	s__Pseudomonas_E alcaliphila_B	78.4218	314	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7502	96.52	96.24	0.87	0.86	3	-
GCF_900102635.1	s__Pseudomonas_E chengduensis	78.3878	319	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	99.23	98.24	0.94	0.89	5	-
GCF_900106015.1	s__Pseudomonas_E sihuiensis	78.3726	318	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_001592875.1	s__Pseudomonas_E sp001592875	78.232	332	1175	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	78.2009	321	1175	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_900111835.1	s__Pseudomonas_F otitidis	78.143	284	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.35	95.43	0.89	0.84	21	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	78.1103	301	1175	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_000474255.1	s__Pseudomonas_F alcaligenes_A	78.1026	311	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.08	97.69	0.89	0.89	3	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	78.0925	330	1175	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_900115695.1	s__Pseudomonas_E toyotomiensis	78.0719	320	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.1942	98.17	97.23	0.91	0.85	7	-
GCF_900114065.1	s__Pseudomonas_A kunmingensis	78.0358	222	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.31	97.18	0.87	0.86	3	-
GCF_015637705.1	s__Pseudomonas_E sp015637705	78.0028	248	1175	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	77.9941	307	1175	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_900112375.1	s__Pseudomonas citronellolis	77.9046	280	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_004521985.1	s__Pseudomonas_E khazarica	77.8199	320	1175	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_900109175.1	s__Pseudomonas_K linyingensis	77.7444	264	1175	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_000689415.1	s__Pseudomonas knackmussii	77.7236	289	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.27	98.27	0.91	0.91	2	-
GCF_000412695.1	s__Pseudomonas_F resinovorans_A	77.7151	290	1175	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_016009175.1	s__Pseudomonas_E alkylphenolica_B	77.6575	214	1175	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_000259195.1	s__Pseudomonas_E donghuensis	77.6504	256	1175	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_009861525.1	s__Pseudomonas_E sp009861525	77.6377	241	1175	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_013523165.1	s__Pseudomonas_E entomophila_A	77.509	203	1175	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_009905435.1	s__Pseudomonas_E sp009905435	77.4886	225	1175	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_012975065.1	s__Pseudomonas_E sp012975065	77.3734	233	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.74	0.94	0.94	3	-
GCF_000820515.1	s__Pseudomonas_E batumici	77.34	242	1175	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_012728315.1	s__Pseudomonas_C sp012728315	76.3596	61	1175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:18:24,353] [INFO] GTDB search result was written to GCF_022601735.1_ASM2260173v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:24,354] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:24,358] [INFO] DFAST_QC result json was written to GCF_022601735.1_ASM2260173v1_genomic.fna/dqc_result.json
[2024-01-25 18:18:24,358] [INFO] DFAST_QC completed!
[2024-01-25 18:18:24,358] [INFO] Total running time: 0h1m34s