[2024-01-24 11:20:49,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,834] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,835] [INFO] DQC Reference Directory: /var/lib/cwl/stgd100783d-4489-4d04-af2f-990cda90d01a/dqc_reference
[2024-01-24 11:20:51,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,023] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg07ae5943-e554-4a3a-b71f-7371ceb3d00e/GCF_014118685.1_ASM1411868v1_genomic.fna.gz | prodigal -d GCF_014118685.1_ASM1411868v1_genomic.fna/cds.fna -a GCF_014118685.1_ASM1411868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:58,343] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:58,344] [INFO] Task started: HMMsearch
[2024-01-24 11:20:58,344] [INFO] Running command: hmmsearch --tblout GCF_014118685.1_ASM1411868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd100783d-4489-4d04-af2f-990cda90d01a/dqc_reference/reference_markers.hmm GCF_014118685.1_ASM1411868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:58,562] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:58,563] [INFO] Found 6/6 markers.
[2024-01-24 11:20:58,588] [INFO] Query marker FASTA was written to GCF_014118685.1_ASM1411868v1_genomic.fna/markers.fasta
[2024-01-24 11:20:58,588] [INFO] Task started: Blastn
[2024-01-24 11:20:58,588] [INFO] Running command: blastn -query GCF_014118685.1_ASM1411868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd100783d-4489-4d04-af2f-990cda90d01a/dqc_reference/reference_markers.fasta -out GCF_014118685.1_ASM1411868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:59,434] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:59,438] [INFO] Selected 18 target genomes.
[2024-01-24 11:20:59,439] [INFO] Target genome list was writen to GCF_014118685.1_ASM1411868v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:59,467] [INFO] Task started: fastANI
[2024-01-24 11:20:59,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ae5943-e554-4a3a-b71f-7371ceb3d00e/GCF_014118685.1_ASM1411868v1_genomic.fna.gz --refList GCF_014118685.1_ASM1411868v1_genomic.fna/target_genomes.txt --output GCF_014118685.1_ASM1411868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:10,081] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:10,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd100783d-4489-4d04-af2f-990cda90d01a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:10,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd100783d-4489-4d04-af2f-990cda90d01a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:10,097] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:10,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:10,098] [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
Flaviflexus huanghaiensis	strain=CICC 10486	GCA_014118685.1	1111473	1111473	type	True	100.0	806	807	95	conclusive
Flaviflexus salsibiostraticola	strain=KCTC 33148	GCA_003952265.1	1282737	1282737	type	True	83.0929	615	807	95	below_threshold
Flaviflexus equikiangi	strain=dk850	GCA_014069875.1	2758573	2758573	type	True	79.0865	340	807	95	below_threshold
Flaviflexus ciconiae	strain=H23T48	GCA_003971195.1	2496867	2496867	type	True	78.6131	245	807	95	below_threshold
Flaviflexus massiliensis	strain=SIT4	GCA_001375495.1	1522309	1522309	type	True	77.8966	217	807	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	76.9781	98	807	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.8222	97	807	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	76.7152	63	807	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.6351	66	807	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	76.5584	110	807	95	below_threshold
Sanguibacter inulinus	strain=DSM 100099	GCA_013415325.1	60922	60922	type	True	76.4828	70	807	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	76.3754	75	807	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	76.0509	52	807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:10,099] [INFO] DFAST Taxonomy check result was written to GCF_014118685.1_ASM1411868v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:10,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:10,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:10,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd100783d-4489-4d04-af2f-990cda90d01a/dqc_reference/checkm_data
[2024-01-24 11:21:10,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:10,126] [INFO] Task started: CheckM
[2024-01-24 11:21:10,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014118685.1_ASM1411868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014118685.1_ASM1411868v1_genomic.fna/checkm_input GCF_014118685.1_ASM1411868v1_genomic.fna/checkm_result
[2024-01-24 11:21:36,728] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:36,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:36,750] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:36,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:36,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014118685.1_ASM1411868v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:36,751] [INFO] Task started: Blastn
[2024-01-24 11:21:36,751] [INFO] Running command: blastn -query GCF_014118685.1_ASM1411868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd100783d-4489-4d04-af2f-990cda90d01a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014118685.1_ASM1411868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:37,990] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:37,994] [INFO] Selected 15 target genomes.
[2024-01-24 11:21:37,994] [INFO] Target genome list was writen to GCF_014118685.1_ASM1411868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:38,007] [INFO] Task started: fastANI
[2024-01-24 11:21:38,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ae5943-e554-4a3a-b71f-7371ceb3d00e/GCF_014118685.1_ASM1411868v1_genomic.fna.gz --refList GCF_014118685.1_ASM1411868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014118685.1_ASM1411868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:45,392] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:45,408] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:45,408] [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_014118685.1	s__Flaviflexus huanghaiensis	100.0	806	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003952265.1	s__Flaviflexus salsibiostraticola	83.0853	614	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014069875.1	s__Flaviflexus sp014069875	79.0792	341	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	99.13	99.13	0.93	0.93	3	-
GCF_003971195.1	s__Flaviflexus sp003971195	78.6131	245	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001375495.1	s__Flaviflexus massiliensis	77.9125	216	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009730335.1	s__Pauljensenia odontolytica_A	76.9064	50	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.93	96.74	0.95	0.91	4	-
GCF_000411415.1	s__Pauljensenia sp000411415	76.7034	56	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.95	97.15	0.96	0.94	6	-
GCF_002847525.1	s__Pauljensenia odontolytica_B	76.6374	59	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
GCF_000466165.1	s__Peptidiphaga sp000466165	76.5815	72	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Peptidiphaga	95.0	99.10	98.96	0.93	0.91	3	-
GCF_009193175.1	s__Georgenia ruanii	76.5778	109	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	76.4857	84	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_001552375.1	s__Cellulomonas iranensis	76.4016	74	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_018388445.1	s__Cellulomonas sp018388445	76.3273	72	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.55	99.30	0.98	0.97	4	-
GCA_012514545.1	s__Actinotalea sp012514545	75.4881	55	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:45,410] [INFO] GTDB search result was written to GCF_014118685.1_ASM1411868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:45,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:45,414] [INFO] DFAST_QC result json was written to GCF_014118685.1_ASM1411868v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:45,414] [INFO] DFAST_QC completed!
[2024-01-24 11:21:45,414] [INFO] Total running time: 0h0m56s