[2024-01-24 14:06:45,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:45,091] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:45,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg72ed603e-9c0d-405b-a6b0-9763e2a6187e/dqc_reference
[2024-01-24 14:06:46,367] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:46,368] [INFO] Task started: Prodigal
[2024-01-24 14:06:46,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg853f8083-ad4c-482c-abb9-44032f33d028/GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/cds.fna -a GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:57,337] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:57,338] [INFO] Task started: HMMsearch
[2024-01-24 14:06:57,338] [INFO] Running command: hmmsearch --tblout GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72ed603e-9c0d-405b-a6b0-9763e2a6187e/dqc_reference/reference_markers.hmm GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:57,678] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:57,680] [INFO] Found 6/6 markers.
[2024-01-24 14:06:57,710] [INFO] Query marker FASTA was written to GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:57,711] [INFO] Task started: Blastn
[2024-01-24 14:06:57,711] [INFO] Running command: blastn -query GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg72ed603e-9c0d-405b-a6b0-9763e2a6187e/dqc_reference/reference_markers.fasta -out GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:58,657] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:58,661] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:58,661] [INFO] Target genome list was writen to GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:58,682] [INFO] Task started: fastANI
[2024-01-24 14:06:58,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg853f8083-ad4c-482c-abb9-44032f33d028/GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna.gz --refList GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:14,911] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72ed603e-9c0d-405b-a6b0-9763e2a6187e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:14,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72ed603e-9c0d-405b-a6b0-9763e2a6187e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:14,938] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:14,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:14,939] [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
Austwickia chelonae	strain=DSM 44178	GCA_900111385.1	100225	100225	type	True	100.0	1177	1177	95	conclusive
Austwickia chelonae	strain=NBRC 105200	GCA_000298175.1	100225	100225	type	True	99.9804	1161	1177	95	conclusive
Mobilicoccus pelagius	strain=NBRC 104925	GCA_000247995.2	746032	746032	type	True	77.7156	245	1177	95	below_threshold
Mobilicoccus massiliensis	strain=SIT2	GCA_000826525.2	1522310	1522310	type	True	77.6916	241	1177	95	below_threshold
Kineosphaera limosa	strain=NBRC 100340	GCA_000298215.1	111564	111564	type	True	77.4628	234	1177	95	below_threshold
Kineosphaera limosa	strain=DSM 14548	GCA_013409325.1	111564	111564	type	True	77.4406	246	1177	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	77.3717	197	1177	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	77.2957	176	1177	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	77.2744	175	1177	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	77.2724	178	1177	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	77.2234	189	1177	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	77.2107	156	1177	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	77.1819	195	1177	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	77.1693	174	1177	95	below_threshold
Ornithinicoccus halotolerans	strain=EGI 80423	GCA_009602535.1	1748220	1748220	type	True	77.0853	160	1177	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	77.0636	173	1177	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	77.0583	173	1177	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.0371	158	1177	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.0351	181	1177	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	76.8721	168	1177	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	76.7054	121	1177	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	76.3892	174	1177	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	76.3771	165	1177	95	below_threshold
Kineosporia mesophila	strain=JCM 16902	GCA_021129235.1	566012	566012	type	True	76.314	161	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,941] [INFO] DFAST Taxonomy check result was written to GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:07:14,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:14,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:14,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72ed603e-9c0d-405b-a6b0-9763e2a6187e/dqc_reference/checkm_data
[2024-01-24 14:07:14,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:14,983] [INFO] Task started: CheckM
[2024-01-24 14:07:14,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/checkm_input GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:07:52,425] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:52,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:52,448] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:52,448] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:52,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:07:52,450] [INFO] Task started: Blastn
[2024-01-24 14:07:52,450] [INFO] Running command: blastn -query GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg72ed603e-9c0d-405b-a6b0-9763e2a6187e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:53,771] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:53,775] [INFO] Selected 17 target genomes.
[2024-01-24 14:07:53,775] [INFO] Target genome list was writen to GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:53,790] [INFO] Task started: fastANI
[2024-01-24 14:07:53,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg853f8083-ad4c-482c-abb9-44032f33d028/GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna.gz --refList GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:05,526] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:05,541] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:05,541] [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_000298175.1	s__Austwickia chelonae	99.9804	1161	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Austwickia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003391095.1	s__Austwickia chelonae_A	85.8366	976	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Austwickia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699675.1	s__Austwickia sp016699675	78.6607	385	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Austwickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001515525.1	s__Piscicoccus intestinalis	77.7273	227	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Piscicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000247995.1	s__Mobilicoccus pelagius	77.7019	246	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826525.2	s__Mobilicoccus massiliensis	77.6779	242	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_006716205.1	s__Oryzihumus leptocrescens	77.5373	214	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_013408565.1	s__Janibacter alkaliphilus	77.4104	191	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014857905.1	s__JACYXE01 sp014857905	77.3823	236	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JACYXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111375.1	s__Pedococcus cremeus	77.3577	198	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_001570945.1	s__Janibacter anophelis	77.1693	174	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_003721155.3	s__Marihabitans melonis	77.0998	187	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_004526345.1	s__Serinicoccus flavus	77.0586	172	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013002715.1	s__Flexivirga aerilata	77.0583	173	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_001428065.1	s__Phycicoccus sp001428065	77.0156	181	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_004168625.1	s__Cellulomonas sp004168625	76.5806	114	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018499875.1	s__Kineosporia sp018499875	76.3777	165	1177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:05,543] [INFO] GTDB search result was written to GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:05,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:05,548] [INFO] DFAST_QC result json was written to GCF_900111385.1_IMG-taxon_2687453746_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:08:05,548] [INFO] DFAST_QC completed!
[2024-01-24 14:08:05,548] [INFO] Total running time: 0h1m20s