[2024-01-25 18:08:05,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:05,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:05,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg179893a4-6f7c-4fa6-9c3d-c5288ca417c4/dqc_reference
[2024-01-25 18:08:06,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:06,680] [INFO] Task started: Prodigal
[2024-01-25 18:08:06,680] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc1a83e4-ee5a-45c3-8154-dac3bb2b67a7/GCF_002934685.1_ASM293468v1_genomic.fna.gz | prodigal -d GCF_002934685.1_ASM293468v1_genomic.fna/cds.fna -a GCF_002934685.1_ASM293468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:24,027] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:24,027] [INFO] Task started: HMMsearch
[2024-01-25 18:08:24,027] [INFO] Running command: hmmsearch --tblout GCF_002934685.1_ASM293468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg179893a4-6f7c-4fa6-9c3d-c5288ca417c4/dqc_reference/reference_markers.hmm GCF_002934685.1_ASM293468v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:24,335] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:24,336] [INFO] Found 6/6 markers.
[2024-01-25 18:08:24,387] [INFO] Query marker FASTA was written to GCF_002934685.1_ASM293468v1_genomic.fna/markers.fasta
[2024-01-25 18:08:24,387] [INFO] Task started: Blastn
[2024-01-25 18:08:24,388] [INFO] Running command: blastn -query GCF_002934685.1_ASM293468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg179893a4-6f7c-4fa6-9c3d-c5288ca417c4/dqc_reference/reference_markers.fasta -out GCF_002934685.1_ASM293468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:25,205] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:25,209] [INFO] Selected 24 target genomes.
[2024-01-25 18:08:25,209] [INFO] Target genome list was writen to GCF_002934685.1_ASM293468v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:25,262] [INFO] Task started: fastANI
[2024-01-25 18:08:25,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc1a83e4-ee5a-45c3-8154-dac3bb2b67a7/GCF_002934685.1_ASM293468v1_genomic.fna.gz --refList GCF_002934685.1_ASM293468v1_genomic.fna/target_genomes.txt --output GCF_002934685.1_ASM293468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:56,146] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:56,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg179893a4-6f7c-4fa6-9c3d-c5288ca417c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:56,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg179893a4-6f7c-4fa6-9c3d-c5288ca417c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:56,160] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:56,160] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:56,160] [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 bohemica	strain=IA19	GCA_002934685.1	2044872	2044872	type	True	100.0	2109	2111	95	conclusive
Pseudomonas abietaniphila	strain=ATCC 700689	GCA_900100795.1	89065	89065	type	True	85.0513	1438	2111	95	below_threshold
Pseudomonas graminis	strain=DSM 11363	GCA_900111735.1	158627	158627	suspected-type	True	83.6642	1251	2111	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	81.3932	994	2111	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	81.3756	910	2111	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	81.3538	1009	2111	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	81.3418	936	2111	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	81.3176	940	2111	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	81.3174	960	2111	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	81.304	740	2111	95	below_threshold
Pseudomonas syringae pv. coryli	strain=NCPPB 4273	GCA_000972175.1	317659	317659	pathovar	True	81.2696	936	2111	95	below_threshold
Pseudomonas viridiflava	strain=ICMP 2848	GCA_001642795.1	33069	33069	type	True	81.2515	976	2111	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	81.1927	945	2111	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	81.1772	895	2111	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	81.1716	926	2111	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	81.0382	911	2111	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	80.92	942	2111	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	80.872	912	2111	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	80.7066	843	2111	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	80.5938	858	2111	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	80.355	832	2111	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	80.3448	806	2111	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	80.2141	850	2111	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	80.1082	781	2111	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:56,162] [INFO] DFAST Taxonomy check result was written to GCF_002934685.1_ASM293468v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:56,162] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:56,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:56,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg179893a4-6f7c-4fa6-9c3d-c5288ca417c4/dqc_reference/checkm_data
[2024-01-25 18:08:56,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:56,225] [INFO] Task started: CheckM
[2024-01-25 18:08:56,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002934685.1_ASM293468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002934685.1_ASM293468v1_genomic.fna/checkm_input GCF_002934685.1_ASM293468v1_genomic.fna/checkm_result
[2024-01-25 18:09:45,283] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:45,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:45,307] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:45,307] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:45,308] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002934685.1_ASM293468v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:45,309] [INFO] Task started: Blastn
[2024-01-25 18:09:45,309] [INFO] Running command: blastn -query GCF_002934685.1_ASM293468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg179893a4-6f7c-4fa6-9c3d-c5288ca417c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002934685.1_ASM293468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:46,675] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:46,677] [INFO] Selected 19 target genomes.
[2024-01-25 18:09:46,678] [INFO] Target genome list was writen to GCF_002934685.1_ASM293468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:46,700] [INFO] Task started: fastANI
[2024-01-25 18:09:46,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc1a83e4-ee5a-45c3-8154-dac3bb2b67a7/GCF_002934685.1_ASM293468v1_genomic.fna.gz --refList GCF_002934685.1_ASM293468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002934685.1_ASM293468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:12,618] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:12,629] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:12,629] [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_002934685.1	s__Pseudomonas_E bohemica	100.0	2109	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002419965.1	s__Pseudomonas_E sp002419965	86.4995	1529	2111	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_004364435.1	s__Pseudomonas_E sp004364435	86.0114	1397	2111	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_009905615.1	s__Pseudomonas_E sp009905615	85.6257	1477	2111	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_002080045.1	s__Pseudomonas_E sp002080045	85.5154	1512	2111	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_003605735.1	s__Pseudomonas_E sp003605735	85.1839	1419	2111	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_900100795.1	s__Pseudomonas_E abietaniphila	85.049	1438	2111	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_002338065.1	s__Pseudomonas_E sp002338065	84.7588	1386	2111	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_900110765.1	s__Pseudomonas_E sp900110765	84.6581	1341	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.34	98.33	0.91	0.90	3	-
GCF_900108875.1	s__Pseudomonas_E sp900108875	84.1915	1357	2111	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_004364335.1	s__Pseudomonas_E graminis_D	83.6311	1303	2111	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_000759445.1	s__Pseudomonas_E lutea	82.7151	1202	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.91	0.91	2	-
GCF_001293775.1	s__Pseudomonas_E syringae_P	80.8422	925	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.87	99.84	0.98	0.97	3	-
GCF_000612585.1	s__Pseudomonas_E sp000612585	80.7585	953	2111	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_001647715.1	s__Pseudomonas_E antarctica_A	80.5871	929	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_009908285.1	s__Pseudomonas_E sp009908285	80.5867	898	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.16	99.16	0.95	0.95	2	-
GCF_015680235.1	s__Pseudomonas_E guariconensis_A	80.1285	704	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.73	0.91	0.90	4	-
GCF_000378945.1	s__Methyloversatilis universalis_A	75.8011	86	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Methyloversatilis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302315.1	s__Zoogloea sp017302315	75.4139	70	2111	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:12,631] [INFO] GTDB search result was written to GCF_002934685.1_ASM293468v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:12,632] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:12,636] [INFO] DFAST_QC result json was written to GCF_002934685.1_ASM293468v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:12,636] [INFO] DFAST_QC completed!
[2024-01-25 18:10:12,637] [INFO] Total running time: 0h2m7s