[2024-01-24 13:46:10,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:10,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:10,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg96e6a973-662a-4364-afee-1c654ce7d3b1/dqc_reference
[2024-01-24 13:46:12,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,223] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,224] [INFO] Running command: gunzip -c /var/lib/cwl/stge7aedaa8-2f6f-46bd-820e-e39b629feadf/GCF_013408565.1_ASM1340856v1_genomic.fna.gz | prodigal -d GCF_013408565.1_ASM1340856v1_genomic.fna/cds.fna -a GCF_013408565.1_ASM1340856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:21,847] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:21,847] [INFO] Task started: HMMsearch
[2024-01-24 13:46:21,847] [INFO] Running command: hmmsearch --tblout GCF_013408565.1_ASM1340856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96e6a973-662a-4364-afee-1c654ce7d3b1/dqc_reference/reference_markers.hmm GCF_013408565.1_ASM1340856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:22,125] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:22,126] [INFO] Found 6/6 markers.
[2024-01-24 13:46:22,156] [INFO] Query marker FASTA was written to GCF_013408565.1_ASM1340856v1_genomic.fna/markers.fasta
[2024-01-24 13:46:22,157] [INFO] Task started: Blastn
[2024-01-24 13:46:22,157] [INFO] Running command: blastn -query GCF_013408565.1_ASM1340856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96e6a973-662a-4364-afee-1c654ce7d3b1/dqc_reference/reference_markers.fasta -out GCF_013408565.1_ASM1340856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:23,692] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:23,700] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:23,701] [INFO] Target genome list was writen to GCF_013408565.1_ASM1340856v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:23,730] [INFO] Task started: fastANI
[2024-01-24 13:46:23,731] [INFO] Running command: fastANI --query /var/lib/cwl/stge7aedaa8-2f6f-46bd-820e-e39b629feadf/GCF_013408565.1_ASM1340856v1_genomic.fna.gz --refList GCF_013408565.1_ASM1340856v1_genomic.fna/target_genomes.txt --output GCF_013408565.1_ASM1340856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:40,600] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:40,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96e6a973-662a-4364-afee-1c654ce7d3b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:40,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96e6a973-662a-4364-afee-1c654ce7d3b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:40,617] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:40,617] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:40,618] [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 indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	81.6342	694	1107	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	81.6256	624	1107	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	81.6067	649	1107	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	81.5362	620	1107	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	81.455	631	1107	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	81.4408	660	1107	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	81.3842	701	1107	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	81.2365	570	1107	95	below_threshold
Janibacter cremeus	strain=DSM 26154	GCA_013409205.1	1285192	1285192	type	True	80.9053	574	1107	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	80.6941	588	1107	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	79.6256	496	1107	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	79.6115	491	1107	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	79.6016	542	1107	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	79.5504	542	1107	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	79.4144	577	1107	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	78.7805	430	1107	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.5552	436	1107	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	77.6997	435	1107	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.4631	278	1107	95	below_threshold
Planobispora rosea	strain=JCM 3166	GCA_014648175.1	35762	35762	type	True	76.5589	383	1107	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	76.5375	384	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:40,620] [INFO] DFAST Taxonomy check result was written to GCF_013408565.1_ASM1340856v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:40,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:40,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:40,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96e6a973-662a-4364-afee-1c654ce7d3b1/dqc_reference/checkm_data
[2024-01-24 13:46:40,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:40,661] [INFO] Task started: CheckM
[2024-01-24 13:46:40,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408565.1_ASM1340856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408565.1_ASM1340856v1_genomic.fna/checkm_input GCF_013408565.1_ASM1340856v1_genomic.fna/checkm_result
[2024-01-24 13:47:30,902] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:30,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:30,924] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:30,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:30,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408565.1_ASM1340856v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:30,925] [INFO] Task started: Blastn
[2024-01-24 13:47:30,925] [INFO] Running command: blastn -query GCF_013408565.1_ASM1340856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96e6a973-662a-4364-afee-1c654ce7d3b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408565.1_ASM1340856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:33,461] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:33,465] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:33,465] [INFO] Target genome list was writen to GCF_013408565.1_ASM1340856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:33,493] [INFO] Task started: fastANI
[2024-01-24 13:47:33,493] [INFO] Running command: fastANI --query /var/lib/cwl/stge7aedaa8-2f6f-46bd-820e-e39b629feadf/GCF_013408565.1_ASM1340856v1_genomic.fna.gz --refList GCF_013408565.1_ASM1340856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408565.1_ASM1340856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:48,441] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:48,469] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:48,470] [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_013408565.1	s__Janibacter alkaliphilus	100.0	1107	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000297495.1	s__Janibacter hoylei	81.6742	621	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCF_900176385.1	s__Janibacter indicus	81.6544	692	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	97.60	97.16	0.90	0.88	4	-
GCF_003721155.3	s__Marihabitans melonis	81.6154	691	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_016888335.1	s__Marihabitans sp016888335	81.5141	623	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570945.1	s__Janibacter anophelis	81.4658	629	1107	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	81.377	667	1107	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	81.2446	648	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409205.1	s__Janibacter cremeus	80.8638	578	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428305.1	s__Janibacter sp001428305	80.7002	633	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570985.1	s__Janibacter limosus	80.6729	590	1107	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	79.6369	534	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_004025965.2	s__Phycicoccus flavus	79.5968	542	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428065.1	s__Phycicoccus sp001428065	79.5373	512	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887965.1	s__Phycicoccus sp016887965	79.3979	575	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011383005.1	s__Phycicoccus sp011383005	79.3801	566	1107	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	79.3478	430	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	76.5283	390	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:48,471] [INFO] GTDB search result was written to GCF_013408565.1_ASM1340856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:48,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:48,483] [INFO] DFAST_QC result json was written to GCF_013408565.1_ASM1340856v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:48,483] [INFO] DFAST_QC completed!
[2024-01-24 13:47:48,483] [INFO] Total running time: 0h1m38s