[2024-01-25 19:44:50,955] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:50,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:50,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e0ad1ef-8574-4285-96b8-692d9f3b7a0b/dqc_reference
[2024-01-25 19:44:52,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:52,128] [INFO] Task started: Prodigal
[2024-01-25 19:44:52,128] [INFO] Running command: gunzip -c /var/lib/cwl/stgd171c8ff-a41d-4702-9933-3d8ef7fbc1fe/GCF_021147775.1_ASM2114777v1_genomic.fna.gz | prodigal -d GCF_021147775.1_ASM2114777v1_genomic.fna/cds.fna -a GCF_021147775.1_ASM2114777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:09,559] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:09,559] [INFO] Task started: HMMsearch
[2024-01-25 19:45:09,560] [INFO] Running command: hmmsearch --tblout GCF_021147775.1_ASM2114777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e0ad1ef-8574-4285-96b8-692d9f3b7a0b/dqc_reference/reference_markers.hmm GCF_021147775.1_ASM2114777v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:09,862] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:09,863] [INFO] Found 6/6 markers.
[2024-01-25 19:45:09,913] [INFO] Query marker FASTA was written to GCF_021147775.1_ASM2114777v1_genomic.fna/markers.fasta
[2024-01-25 19:45:09,914] [INFO] Task started: Blastn
[2024-01-25 19:45:09,914] [INFO] Running command: blastn -query GCF_021147775.1_ASM2114777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e0ad1ef-8574-4285-96b8-692d9f3b7a0b/dqc_reference/reference_markers.fasta -out GCF_021147775.1_ASM2114777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:10,713] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:10,715] [INFO] Selected 23 target genomes.
[2024-01-25 19:45:10,715] [INFO] Target genome list was writen to GCF_021147775.1_ASM2114777v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:10,744] [INFO] Task started: fastANI
[2024-01-25 19:45:10,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgd171c8ff-a41d-4702-9933-3d8ef7fbc1fe/GCF_021147775.1_ASM2114777v1_genomic.fna.gz --refList GCF_021147775.1_ASM2114777v1_genomic.fna/target_genomes.txt --output GCF_021147775.1_ASM2114777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:36,051] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:36,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e0ad1ef-8574-4285-96b8-692d9f3b7a0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:36,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e0ad1ef-8574-4285-96b8-692d9f3b7a0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:36,078] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:45:36,079] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:45:36,079] [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 syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	84.1283	1304	2031	95	below_threshold
Pseudomonas viridiflava	strain=ICMP2848	GCA_001401215.1	33069	33069	type	True	84.1164	1300	2031	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	84.0989	1254	2031	95	below_threshold
Pseudomonas viridiflava	strain=ICMP 2848	GCA_001642795.1	33069	33069	type	True	84.0916	1367	2031	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	84.0881	1319	2031	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	83.7745	1310	2031	95	below_threshold
Pseudomonas syringae	strain=NCPPB 3739	GCA_000233835.2	317	317	pathovar	True	83.7568	1122	2031	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP529	GCA_001400335.1	251701	251701	pathovar	True	83.7418	1233	2031	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	83.6349	1313	2031	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	83.621	1333	2031	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	83.6109	1294	2031	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4303	GCA_001401395.1	251701	251701	pathovar	True	83.5556	1273	2031	95	below_threshold
Pseudomonas ficuserectae	strain=ICMP7848	GCA_001400815.1	53410	53410	type	True	83.3342	1116	2031	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	83.3114	974	2031	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	83.1878	1315	2031	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	83.0668	1341	2031	95	below_threshold
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	82.5731	1130	2031	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	82.5222	1133	2031	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	79.9023	581	2031	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	79.6397	628	2031	95	below_threshold
[Pseudomonas] urumqiensis	strain=T3	GCA_003640395.1	638269	638269	type	True	77.7564	367	2031	95	below_threshold
Thiopseudomonas denitrificans	strain=DSM 28679	GCA_004363035.1	1501432	1501432	type	True	77.2457	170	2031	95	below_threshold
Thiopseudomonas denitrificans	strain=X2	GCA_002866065.1	1501432	1501432	type	True	77.1938	173	2031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:36,080] [INFO] DFAST Taxonomy check result was written to GCF_021147775.1_ASM2114777v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:36,081] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:36,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:36,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e0ad1ef-8574-4285-96b8-692d9f3b7a0b/dqc_reference/checkm_data
[2024-01-25 19:45:36,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:36,157] [INFO] Task started: CheckM
[2024-01-25 19:45:36,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021147775.1_ASM2114777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021147775.1_ASM2114777v1_genomic.fna/checkm_input GCF_021147775.1_ASM2114777v1_genomic.fna/checkm_result
[2024-01-25 19:46:28,913] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:28,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:28,936] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:28,937] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:28,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021147775.1_ASM2114777v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:28,938] [INFO] Task started: Blastn
[2024-01-25 19:46:28,938] [INFO] Running command: blastn -query GCF_021147775.1_ASM2114777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e0ad1ef-8574-4285-96b8-692d9f3b7a0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_021147775.1_ASM2114777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:30,341] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:30,347] [INFO] Selected 19 target genomes.
[2024-01-25 19:46:30,347] [INFO] Target genome list was writen to GCF_021147775.1_ASM2114777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:30,372] [INFO] Task started: fastANI
[2024-01-25 19:46:30,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgd171c8ff-a41d-4702-9933-3d8ef7fbc1fe/GCF_021147775.1_ASM2114777v1_genomic.fna.gz --refList GCF_021147775.1_ASM2114777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021147775.1_ASM2114777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:56,691] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:56,702] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:46:56,703] [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_001642795.1	s__Pseudomonas_E viridiflava	84.1024	1365	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	96.41	0.93	0.89	1379	-
GCF_900143095.1	s__Pseudomonas_E asturiensis	83.8634	1409	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.96	0.95	0.95	2	-
GCF_000444135.1	s__Pseudomonas_E avellanae	83.8467	1216	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.46	0.87	0.79	302	-
GCF_014358015.1	s__Pseudomonas_E triticumensis	83.7675	1336	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.53	98.52	0.94	0.92	3	-
GCF_002723575.1	s__Pseudomonas_E viridiflava_B	83.7534	1344	2031	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_002087235.1	s__Pseudomonas_E floridensis	83.7232	1301	2031	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_003702045.1	s__Pseudomonas_E viridiflava_C	83.6732	1276	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.39	99.39	0.95	0.95	2	-
GCF_900100365.1	s__Pseudomonas_E cannabina	83.6464	1312	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.50	95.44	0.90	0.84	17	-
GCF_002699855.1	s__Pseudomonas_E amygdali	83.4793	1205	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	96.47	0.89	0.82	226	-
GCF_001293775.1	s__Pseudomonas_E syringae_P	83.4767	1281	2031	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_001466965.1	s__Pseudomonas_E syringae_Q	83.4624	1231	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.91	98.87	0.94	0.94	3	-
GCF_900103225.1	s__Pseudomonas_E congelans	83.3398	1241	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.60	98.04	0.95	0.92	20	-
GCF_000452705.1	s__Pseudomonas_E syringae_F	83.3235	1245	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.97	98.97	0.94	0.94	2	-
GCF_001400735.1	s__Pseudomonas_E caricapapayae	83.2227	1273	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	97.41	0.91	0.88	11	-
GCF_002093745.1	s__Pseudomonas_E graminis_C	83.2192	1231	2031	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_001401155.1	s__Pseudomonas_E tremae	83.0913	1215	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.42	0.92	0.88	76	-
GCF_001647715.1	s__Pseudomonas_E antarctica_A	80.1152	812	2031	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_009932375.1	s__Pseudomonas_E juntendi	79.4717	587	2031	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:56,704] [INFO] GTDB search result was written to GCF_021147775.1_ASM2114777v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:56,705] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:56,708] [INFO] DFAST_QC result json was written to GCF_021147775.1_ASM2114777v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:56,709] [INFO] DFAST_QC completed!
[2024-01-25 19:46:56,709] [INFO] Total running time: 0h2m6s