[2024-01-24 11:13:49,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg74639ea6-5c2c-4586-bee4-93df25b9e4a5/dqc_reference
[2024-01-24 11:13:50,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,876] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,876] [INFO] Running command: gunzip -c /var/lib/cwl/stgd50aa8e5-d0c9-410b-849c-a7467e16b5df/GCF_006715095.1_ASM671509v1_genomic.fna.gz | prodigal -d GCF_006715095.1_ASM671509v1_genomic.fna/cds.fna -a GCF_006715095.1_ASM671509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:01,904] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:01,905] [INFO] Task started: HMMsearch
[2024-01-24 11:14:01,905] [INFO] Running command: hmmsearch --tblout GCF_006715095.1_ASM671509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74639ea6-5c2c-4586-bee4-93df25b9e4a5/dqc_reference/reference_markers.hmm GCF_006715095.1_ASM671509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:02,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:02,154] [INFO] Found 6/6 markers.
[2024-01-24 11:14:02,188] [INFO] Query marker FASTA was written to GCF_006715095.1_ASM671509v1_genomic.fna/markers.fasta
[2024-01-24 11:14:02,189] [INFO] Task started: Blastn
[2024-01-24 11:14:02,189] [INFO] Running command: blastn -query GCF_006715095.1_ASM671509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74639ea6-5c2c-4586-bee4-93df25b9e4a5/dqc_reference/reference_markers.fasta -out GCF_006715095.1_ASM671509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:03,394] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:03,397] [INFO] Selected 20 target genomes.
[2024-01-24 11:14:03,398] [INFO] Target genome list was writen to GCF_006715095.1_ASM671509v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:03,407] [INFO] Task started: fastANI
[2024-01-24 11:14:03,407] [INFO] Running command: fastANI --query /var/lib/cwl/stgd50aa8e5-d0c9-410b-849c-a7467e16b5df/GCF_006715095.1_ASM671509v1_genomic.fna.gz --refList GCF_006715095.1_ASM671509v1_genomic.fna/target_genomes.txt --output GCF_006715095.1_ASM671509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:16,644] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:16,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74639ea6-5c2c-4586-bee4-93df25b9e4a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:16,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74639ea6-5c2c-4586-bee4-93df25b9e4a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:16,664] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:14:16,664] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:14:16,664] [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
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	79.5174	476	1177	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	79.3646	459	1177	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	79.3101	474	1177	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	79.2399	485	1177	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.8666	307	1177	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	78.866	415	1177	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	78.8592	426	1177	95	below_threshold
Flexivirga endophytica	strain=CGMCC 1.15085	GCA_014640635.1	1849103	1849103	type	True	78.6962	398	1177	95	below_threshold
Dermacoccus nishinomiyaensis	strain=FDAARGOS_1119	GCA_016766835.1	1274	1274	type	True	78.6945	315	1177	95	below_threshold
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	78.6531	406	1177	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	78.6228	321	1177	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.5252	347	1177	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.3807	317	1177	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	78.3572	300	1177	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.1963	293	1177	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	78.0885	265	1177	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.7858	279	1177	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	77.078	212	1177	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	76.9896	252	1177	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	76.7894	213	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:16,665] [INFO] DFAST Taxonomy check result was written to GCF_006715095.1_ASM671509v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:16,666] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:16,666] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:16,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74639ea6-5c2c-4586-bee4-93df25b9e4a5/dqc_reference/checkm_data
[2024-01-24 11:14:16,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:16,701] [INFO] Task started: CheckM
[2024-01-24 11:14:16,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006715095.1_ASM671509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006715095.1_ASM671509v1_genomic.fna/checkm_input GCF_006715095.1_ASM671509v1_genomic.fna/checkm_result
[2024-01-24 11:15:04,662] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:04,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:04,685] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:04,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:04,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006715095.1_ASM671509v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:04,686] [INFO] Task started: Blastn
[2024-01-24 11:15:04,687] [INFO] Running command: blastn -query GCF_006715095.1_ASM671509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74639ea6-5c2c-4586-bee4-93df25b9e4a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_006715095.1_ASM671509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:06,512] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:06,516] [INFO] Selected 15 target genomes.
[2024-01-24 11:15:06,516] [INFO] Target genome list was writen to GCF_006715095.1_ASM671509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:06,534] [INFO] Task started: fastANI
[2024-01-24 11:15:06,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgd50aa8e5-d0c9-410b-849c-a7467e16b5df/GCF_006715095.1_ASM671509v1_genomic.fna.gz --refList GCF_006715095.1_ASM671509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006715095.1_ASM671509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:19,015] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:19,031] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:19,031] [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_006715095.1	s__Yimella lutea	100.0	1176	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.40	98.40	0.90	0.90	2	conclusive
GCF_003386865.1	s__Yimella indica	84.4643	804	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017654605.1	s__Yimella sp014530045	81.7956	682	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	98.79	97.58	0.96	0.92	3	-
GCF_013135345.1	s__Yimella sp013135345	79.6056	476	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001247745.1	s__Luteipulveratus halotolerans	79.4809	480	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716095.1	s__Barrientosiimonas humi	79.3235	468	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013410455.1	s__Allobranchiibius huperziae	79.2843	382	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	97.04	97.04	0.91	0.91	2	-
GCF_013002715.1	s__Flexivirga aerilata	79.2594	483	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565405.1	s__Allobranchiibius sp017565405	79.0489	393	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.8935	357	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	78.8497	415	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640635.1	s__Flexivirga endophytica	78.6962	398	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002846495.1	s__Phycicoccus duodecadis	78.6105	322	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754615.1	s__Kitasatospora sp002754615	77.1724	258	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014648555.1	s__Kitasatospora griseola	76.97	254	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	97.80	97.68	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:19,033] [INFO] GTDB search result was written to GCF_006715095.1_ASM671509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:19,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:19,038] [INFO] DFAST_QC result json was written to GCF_006715095.1_ASM671509v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:19,038] [INFO] DFAST_QC completed!
[2024-01-24 11:15:19,038] [INFO] Total running time: 0h1m29s