[2024-01-25 20:22:50,658] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:50,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:50,660] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb69299e-9601-4513-85d0-4c5077df02f8/dqc_reference
[2024-01-25 20:22:51,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:51,825] [INFO] Task started: Prodigal
[2024-01-25 20:22:51,826] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8be3630-8e06-4fd0-923d-f5af0c0725bb/GCF_016888335.1_ASM1688833v1_genomic.fna.gz | prodigal -d GCF_016888335.1_ASM1688833v1_genomic.fna/cds.fna -a GCF_016888335.1_ASM1688833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:58,986] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:58,987] [INFO] Task started: HMMsearch
[2024-01-25 20:22:58,987] [INFO] Running command: hmmsearch --tblout GCF_016888335.1_ASM1688833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb69299e-9601-4513-85d0-4c5077df02f8/dqc_reference/reference_markers.hmm GCF_016888335.1_ASM1688833v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:59,181] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:59,182] [INFO] Found 6/6 markers.
[2024-01-25 20:22:59,207] [INFO] Query marker FASTA was written to GCF_016888335.1_ASM1688833v1_genomic.fna/markers.fasta
[2024-01-25 20:22:59,207] [INFO] Task started: Blastn
[2024-01-25 20:22:59,207] [INFO] Running command: blastn -query GCF_016888335.1_ASM1688833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb69299e-9601-4513-85d0-4c5077df02f8/dqc_reference/reference_markers.fasta -out GCF_016888335.1_ASM1688833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:00,390] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:00,392] [INFO] Selected 14 target genomes.
[2024-01-25 20:23:00,392] [INFO] Target genome list was writen to GCF_016888335.1_ASM1688833v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:00,400] [INFO] Task started: fastANI
[2024-01-25 20:23:00,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8be3630-8e06-4fd0-923d-f5af0c0725bb/GCF_016888335.1_ASM1688833v1_genomic.fna.gz --refList GCF_016888335.1_ASM1688833v1_genomic.fna/target_genomes.txt --output GCF_016888335.1_ASM1688833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:11,101] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:11,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb69299e-9601-4513-85d0-4c5077df02f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:11,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb69299e-9601-4513-85d0-4c5077df02f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:11,112] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:11,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:11,112] [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
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	100.0	990	990	95	conclusive
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	84.3781	733	990	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	82.3579	621	990	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	82.2136	577	990	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	82.1938	610	990	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	82.1768	595	990	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	82.0956	630	990	95	below_threshold
Janibacter massiliensis	strain=Marseille-P4121	GCA_900289115.1	2058291	2058291	type	True	80.4177	469	990	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	80.3974	539	990	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	80.3326	534	990	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	79.5828	522	990	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	79.0552	393	990	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.9706	415	990	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.8438	403	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:11,114] [INFO] DFAST Taxonomy check result was written to GCF_016888335.1_ASM1688833v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:11,114] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:11,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:11,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb69299e-9601-4513-85d0-4c5077df02f8/dqc_reference/checkm_data
[2024-01-25 20:23:11,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:11,145] [INFO] Task started: CheckM
[2024-01-25 20:23:11,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016888335.1_ASM1688833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016888335.1_ASM1688833v1_genomic.fna/checkm_input GCF_016888335.1_ASM1688833v1_genomic.fna/checkm_result
[2024-01-25 20:23:53,260] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:53,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:53,287] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:53,288] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:53,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016888335.1_ASM1688833v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:53,289] [INFO] Task started: Blastn
[2024-01-25 20:23:53,289] [INFO] Running command: blastn -query GCF_016888335.1_ASM1688833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb69299e-9601-4513-85d0-4c5077df02f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_016888335.1_ASM1688833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:55,284] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:55,288] [INFO] Selected 13 target genomes.
[2024-01-25 20:23:55,288] [INFO] Target genome list was writen to GCF_016888335.1_ASM1688833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:55,314] [INFO] Task started: fastANI
[2024-01-25 20:23:55,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8be3630-8e06-4fd0-923d-f5af0c0725bb/GCF_016888335.1_ASM1688833v1_genomic.fna.gz --refList GCF_016888335.1_ASM1688833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016888335.1_ASM1688833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:05,534] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:05,542] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:05,543] [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_016888335.1	s__Marihabitans sp016888335	100.0	990	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003721155.3	s__Marihabitans melonis	84.4432	728	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_007828725.1	s__Marihabitans asiaticum	82.9149	656	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176385.1	s__Janibacter indicus	82.3245	624	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	97.60	97.16	0.90	0.88	4	-
GCF_000297495.1	s__Janibacter hoylei	82.2674	573	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCF_001570945.1	s__Janibacter anophelis	82.1949	594	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_001591405.1	s__Janibacter terrae	82.0798	632	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	-
GCF_004295485.1	s__Janibacter limosus_A	81.4646	583	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116945.1	s__Janibacter merdipullorum	81.4561	531	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	80.4442	524	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_013201035.1	s__Phycicoccus sp013201035	80.4166	547	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763705.1	s__Phycicoccus sp014763705	80.0554	410	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139485.1	s__Phycicoccus sp018139485	79.8349	492	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:05,545] [INFO] GTDB search result was written to GCF_016888335.1_ASM1688833v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:05,547] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:05,549] [INFO] DFAST_QC result json was written to GCF_016888335.1_ASM1688833v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:05,550] [INFO] DFAST_QC completed!
[2024-01-25 20:24:05,550] [INFO] Total running time: 0h1m15s