[2024-01-24 12:30:05,382] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,387] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg7897bdd9-4746-48f8-849d-aeaae7ccb9ed/dqc_reference
[2024-01-24 12:30:07,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,247] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,248] [INFO] Running command: gunzip -c /var/lib/cwl/stge5a2bf6b-44c9-4410-8a6d-1a95a7d65998/GCF_900169715.1_PRJEB20004_genomic.fna.gz | prodigal -d GCF_900169715.1_PRJEB20004_genomic.fna/cds.fna -a GCF_900169715.1_PRJEB20004_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:14,117] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:14,118] [INFO] Task started: HMMsearch
[2024-01-24 12:30:14,118] [INFO] Running command: hmmsearch --tblout GCF_900169715.1_PRJEB20004_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7897bdd9-4746-48f8-849d-aeaae7ccb9ed/dqc_reference/reference_markers.hmm GCF_900169715.1_PRJEB20004_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:14,400] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:14,401] [INFO] Found 6/6 markers.
[2024-01-24 12:30:14,421] [INFO] Query marker FASTA was written to GCF_900169715.1_PRJEB20004_genomic.fna/markers.fasta
[2024-01-24 12:30:14,422] [INFO] Task started: Blastn
[2024-01-24 12:30:14,422] [INFO] Running command: blastn -query GCF_900169715.1_PRJEB20004_genomic.fna/markers.fasta -db /var/lib/cwl/stg7897bdd9-4746-48f8-849d-aeaae7ccb9ed/dqc_reference/reference_markers.fasta -out GCF_900169715.1_PRJEB20004_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:15,259] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:15,262] [INFO] Selected 25 target genomes.
[2024-01-24 12:30:15,263] [INFO] Target genome list was writen to GCF_900169715.1_PRJEB20004_genomic.fna/target_genomes.txt
[2024-01-24 12:30:15,287] [INFO] Task started: fastANI
[2024-01-24 12:30:15,287] [INFO] Running command: fastANI --query /var/lib/cwl/stge5a2bf6b-44c9-4410-8a6d-1a95a7d65998/GCF_900169715.1_PRJEB20004_genomic.fna.gz --refList GCF_900169715.1_PRJEB20004_genomic.fna/target_genomes.txt --output GCF_900169715.1_PRJEB20004_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:26,930] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:26,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7897bdd9-4746-48f8-849d-aeaae7ccb9ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:26,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7897bdd9-4746-48f8-849d-aeaae7ccb9ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:26,944] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:26,944] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:26,945] [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
Rothia koreensis	strain=JCM 15915	GCA_004136575.1	592378	592378	type	True	79.1943	300	807	95	below_threshold
Rothia koreensis	strain=JCM 15915	GCA_009734705.1	592378	592378	type	True	79.1624	295	807	95	below_threshold
Rothia kristinae	strain=FDAARGOS_864	GCA_016028855.1	37923	37923	type	True	78.008	190	807	95	below_threshold
Rothia kristinae	strain=ATCC 27570	GCA_004136565.1	37923	37923	type	True	77.8999	184	807	95	below_threshold
Paenarthrobacter ilicis	strain=DSM 20138	GCA_016907545.1	43665	43665	type	True	77.8331	64	807	95	below_threshold
Rothia kristinae	strain=NBRC 15354	GCA_001570865.1	37923	37923	type	True	77.8252	186	807	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	77.5741	118	807	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	77.5123	92	807	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	77.5119	119	807	95	below_threshold
Psychromicrobium silvestre	strain=DSM 102047	GCA_013408295.1	1645614	1645614	type	True	77.4672	57	807	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	77.4357	120	807	95	below_threshold
Kocuria rosea	strain=DSM 20447	GCA_006717035.1	1275	1275	suspected-type	True	77.4228	119	807	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	77.2977	121	807	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	77.2337	111	807	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	77.2122	90	807	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	76.8968	94	807	95	below_threshold
Nesterenkonia aurantiaca	strain=DSM 27373	GCA_004364585.1	1436010	1436010	type	True	76.7535	56	807	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	76.6512	91	807	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	76.5597	51	807	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	76.4539	53	807	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.4039	53	807	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	76.1316	52	807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:26,946] [INFO] DFAST Taxonomy check result was written to GCF_900169715.1_PRJEB20004_genomic.fna/tc_result.tsv
[2024-01-24 12:30:26,947] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:26,947] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:26,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7897bdd9-4746-48f8-849d-aeaae7ccb9ed/dqc_reference/checkm_data
[2024-01-24 12:30:26,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:26,976] [INFO] Task started: CheckM
[2024-01-24 12:30:26,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900169715.1_PRJEB20004_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900169715.1_PRJEB20004_genomic.fna/checkm_input GCF_900169715.1_PRJEB20004_genomic.fna/checkm_result
[2024-01-24 12:30:51,585] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:51,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:51,605] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:51,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:51,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900169715.1_PRJEB20004_genomic.fna/markers.fasta)
[2024-01-24 12:30:51,605] [INFO] Task started: Blastn
[2024-01-24 12:30:51,605] [INFO] Running command: blastn -query GCF_900169715.1_PRJEB20004_genomic.fna/markers.fasta -db /var/lib/cwl/stg7897bdd9-4746-48f8-849d-aeaae7ccb9ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_900169715.1_PRJEB20004_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:52,909] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:52,912] [INFO] Selected 11 target genomes.
[2024-01-24 12:30:52,912] [INFO] Target genome list was writen to GCF_900169715.1_PRJEB20004_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:52,920] [INFO] Task started: fastANI
[2024-01-24 12:30:52,920] [INFO] Running command: fastANI --query /var/lib/cwl/stge5a2bf6b-44c9-4410-8a6d-1a95a7d65998/GCF_900169715.1_PRJEB20004_genomic.fna.gz --refList GCF_900169715.1_PRJEB20004_genomic.fna/target_genomes_gtdb.txt --output GCF_900169715.1_PRJEB20004_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:59,286] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:59,294] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:59,294] [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_900169715.1	s__Rothia massiliensis	100.0	807	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.67	98.66	0.95	0.94	3	conclusive
GCF_000710345.2	s__Rothia sp000710345	80.9048	517	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394385.1	s__Rothia sp004136585	79.2078	290	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.70	99.70	0.98	0.98	2	-
GCF_004136575.1	s__Rothia koreensis	79.1708	302	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.36	98.73	0.95	0.92	3	-
GCF_004137765.1	s__Rothia sp004137765	78.8469	286	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004136635.1	s__Rothia halotolerans	78.2033	226	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570865.1	s__Rothia kristinae	77.8246	186	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.74	96.46	0.96	0.92	16	-
GCF_006094695.1	s__Kocuria rosea	77.5119	119	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_001580365.1	s__Kocuria turfanensis	77.4357	120	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_001483755.1	s__Kocuria polaris_A	77.3306	117	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408295.1	s__Psychromicrobium silvestre	77.2965	56	807	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Psychromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:59,296] [INFO] GTDB search result was written to GCF_900169715.1_PRJEB20004_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:59,296] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:59,299] [INFO] DFAST_QC result json was written to GCF_900169715.1_PRJEB20004_genomic.fna/dqc_result.json
[2024-01-24 12:30:59,300] [INFO] DFAST_QC completed!
[2024-01-24 12:30:59,300] [INFO] Total running time: 0h0m54s