[2024-01-24 11:44:05,457] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg538882ac-99eb-41ca-921d-0fdf602c5b8b/dqc_reference
[2024-01-24 11:44:08,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,841] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,841] [INFO] Running command: gunzip -c /var/lib/cwl/stged60f7f1-be0c-4cbb-adf7-bbbd206aec48/GCF_007431345.1_ASM743134v1_genomic.fna.gz | prodigal -d GCF_007431345.1_ASM743134v1_genomic.fna/cds.fna -a GCF_007431345.1_ASM743134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:27,471] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:27,472] [INFO] Task started: HMMsearch
[2024-01-24 11:44:27,472] [INFO] Running command: hmmsearch --tblout GCF_007431345.1_ASM743134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg538882ac-99eb-41ca-921d-0fdf602c5b8b/dqc_reference/reference_markers.hmm GCF_007431345.1_ASM743134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:27,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:27,785] [INFO] Found 6/6 markers.
[2024-01-24 11:44:27,829] [INFO] Query marker FASTA was written to GCF_007431345.1_ASM743134v1_genomic.fna/markers.fasta
[2024-01-24 11:44:27,830] [INFO] Task started: Blastn
[2024-01-24 11:44:27,830] [INFO] Running command: blastn -query GCF_007431345.1_ASM743134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg538882ac-99eb-41ca-921d-0fdf602c5b8b/dqc_reference/reference_markers.fasta -out GCF_007431345.1_ASM743134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:28,703] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:28,707] [INFO] Selected 42 target genomes.
[2024-01-24 11:44:28,707] [INFO] Target genome list was writen to GCF_007431345.1_ASM743134v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:28,724] [INFO] Task started: fastANI
[2024-01-24 11:44:28,724] [INFO] Running command: fastANI --query /var/lib/cwl/stged60f7f1-be0c-4cbb-adf7-bbbd206aec48/GCF_007431345.1_ASM743134v1_genomic.fna.gz --refList GCF_007431345.1_ASM743134v1_genomic.fna/target_genomes.txt --output GCF_007431345.1_ASM743134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:02,531] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:02,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg538882ac-99eb-41ca-921d-0fdf602c5b8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:02,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg538882ac-99eb-41ca-921d-0fdf602c5b8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:02,555] [INFO] Found 32 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:02,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:02,555] [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
Chitinimonas arctica	strain=R3-44	GCA_007431345.1	2594795	2594795	type	True	100.0	1762	1764	95	conclusive
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	79.6539	589	1764	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	79.4438	712	1764	95	below_threshold
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	77.7383	288	1764	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	77.6303	290	1764	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	77.2805	207	1764	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	77.1866	278	1764	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	77.1003	298	1764	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	76.9692	207	1764	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	76.9295	168	1764	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	76.905	111	1764	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	76.7528	209	1764	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	76.4867	202	1764	95	below_threshold
Paraburkholderia ferrariae	strain=NBRC 106233	GCA_000685035.1	386056	386056	type	True	76.4594	119	1764	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	76.3895	149	1764	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	76.0933	92	1764	95	below_threshold
Chitinivorax tropicus	strain=DSM 27165	GCA_014202905.1	714531	714531	type	True	76.0667	103	1764	95	below_threshold
Aquamicrobium defluvii	strain=DSM 11603	GCA_004363725.1	69279	69279	type	True	76.0456	51	1764	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	76.031	109	1764	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	76.0284	64	1764	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	75.825	64	1764	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.6853	70	1764	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	75.3432	53	1764	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	75.3324	66	1764	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.2549	71	1764	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.1936	60	1764	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	75.1338	54	1764	95	below_threshold
Roseococcus suduntuyensis	strain=DSM 19979	GCA_014196305.1	455361	455361	type	True	74.9173	71	1764	95	below_threshold
Streptomyces caelestis	strain=JCM 4566	GCA_014650295.1	36816	36816	type	True	74.8846	60	1764	95	below_threshold
Streptomyces albus	strain=NBRC 13014	GCA_000813365.1	1888	1888	suspected-type	True	74.7935	62	1764	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	74.7738	63	1764	95	below_threshold
Streptomyces zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	74.705	61	1764	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:02,557] [INFO] DFAST Taxonomy check result was written to GCF_007431345.1_ASM743134v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:02,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:02,557] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:02,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg538882ac-99eb-41ca-921d-0fdf602c5b8b/dqc_reference/checkm_data
[2024-01-24 11:45:02,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:02,607] [INFO] Task started: CheckM
[2024-01-24 11:45:02,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007431345.1_ASM743134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007431345.1_ASM743134v1_genomic.fna/checkm_input GCF_007431345.1_ASM743134v1_genomic.fna/checkm_result
[2024-01-24 11:45:56,461] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:56,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:56,479] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:56,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:56,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007431345.1_ASM743134v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:56,481] [INFO] Task started: Blastn
[2024-01-24 11:45:56,481] [INFO] Running command: blastn -query GCF_007431345.1_ASM743134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg538882ac-99eb-41ca-921d-0fdf602c5b8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007431345.1_ASM743134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:57,941] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:57,945] [INFO] Selected 17 target genomes.
[2024-01-24 11:45:57,945] [INFO] Target genome list was writen to GCF_007431345.1_ASM743134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:57,977] [INFO] Task started: fastANI
[2024-01-24 11:45:57,980] [INFO] Running command: fastANI --query /var/lib/cwl/stged60f7f1-be0c-4cbb-adf7-bbbd206aec48/GCF_007431345.1_ASM743134v1_genomic.fna.gz --refList GCF_007431345.1_ASM743134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007431345.1_ASM743134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:11,790] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:11,805] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:11,805] [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_007431345.1	s__Chitinimonas arctica	100.0	1761	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900119825.1	s__Chitinimonas taiwanensis	79.6495	589	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	96.92	96.91	0.93	0.93	3	-
GCF_000428465.1	s__Chitinimonas koreensis	79.4577	710	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234745.1	s__JAFAKZ01 sp019234745	78.1341	283	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__JAFAKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002735695.1	s__Chitinimonas sp002735695	77.9947	290	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	99.97	99.97	0.99	0.99	2	-
GCA_019084025.1	s__DAT-1 sp019084025	77.8767	188	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__DAT-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015140455.1	s__Jeongeupia sp015140455	77.8468	214	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325475.1	s__Chromobacterium phragmitis	77.6194	291	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_010435965.1	s__STGJ01 sp010435965	77.2795	208	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	77.178	280	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	77.1426	247	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003966565.1	s__UBA2250 sp003966565	76.5658	95	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685035.1	s__Paraburkholderia ferrariae	76.4323	122	1764	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	75.4745	68	1764	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:11,807] [INFO] GTDB search result was written to GCF_007431345.1_ASM743134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:11,808] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:11,813] [INFO] DFAST_QC result json was written to GCF_007431345.1_ASM743134v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:11,813] [INFO] DFAST_QC completed!
[2024-01-24 11:46:11,813] [INFO] Total running time: 0h2m6s