[2024-01-24 14:39:01,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:01,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:01,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg396f9093-9bc1-4368-b0a5-4652f86898ba/dqc_reference
[2024-01-24 14:39:04,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,243] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,243] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0127270-c4c3-44fc-b90b-71bec2fbbaf3/GCF_016918855.1_ASM1691885v1_genomic.fna.gz | prodigal -d GCF_016918855.1_ASM1691885v1_genomic.fna/cds.fna -a GCF_016918855.1_ASM1691885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:33,146] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:33,147] [INFO] Task started: HMMsearch
[2024-01-24 14:39:33,147] [INFO] Running command: hmmsearch --tblout GCF_016918855.1_ASM1691885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg396f9093-9bc1-4368-b0a5-4652f86898ba/dqc_reference/reference_markers.hmm GCF_016918855.1_ASM1691885v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:33,562] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:33,563] [INFO] Found 6/6 markers.
[2024-01-24 14:39:33,661] [INFO] Query marker FASTA was written to GCF_016918855.1_ASM1691885v1_genomic.fna/markers.fasta
[2024-01-24 14:39:33,662] [INFO] Task started: Blastn
[2024-01-24 14:39:33,662] [INFO] Running command: blastn -query GCF_016918855.1_ASM1691885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg396f9093-9bc1-4368-b0a5-4652f86898ba/dqc_reference/reference_markers.fasta -out GCF_016918855.1_ASM1691885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:35,130] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:35,133] [INFO] Selected 19 target genomes.
[2024-01-24 14:39:35,133] [INFO] Target genome list was writen to GCF_016918855.1_ASM1691885v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:35,144] [INFO] Task started: fastANI
[2024-01-24 14:39:35,144] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0127270-c4c3-44fc-b90b-71bec2fbbaf3/GCF_016918855.1_ASM1691885v1_genomic.fna.gz --refList GCF_016918855.1_ASM1691885v1_genomic.fna/target_genomes.txt --output GCF_016918855.1_ASM1691885v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:16,081] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:16,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg396f9093-9bc1-4368-b0a5-4652f86898ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:16,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg396f9093-9bc1-4368-b0a5-4652f86898ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:16,097] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:16,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:16,097] [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
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	100.0	3196	3198	95	conclusive
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	83.4522	1703	3198	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	83.4269	1711	3198	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	83.2522	1359	3198	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	83.1556	1592	3198	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	83.1527	1594	3198	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	82.9238	1615	3198	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	82.9009	1735	3198	95	below_threshold
Actinacidiphila yeochonensis	strain=CN732	GCA_000745345.1	89050	89050	type	True	82.2822	1548	3198	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.8175	1210	3198	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	79.9243	1393	3198	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.8837	1191	3198	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	79.7827	1109	3198	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	79.7731	1098	3198	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	79.7464	1301	3198	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_017916255.1	35621	35621	type	True	79.7249	1160	3198	95	below_threshold
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	79.6676	1144	3198	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	79.5977	1184	3198	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	78.9792	1259	3198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:16,099] [INFO] DFAST Taxonomy check result was written to GCF_016918855.1_ASM1691885v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:16,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:16,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:16,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg396f9093-9bc1-4368-b0a5-4652f86898ba/dqc_reference/checkm_data
[2024-01-24 14:40:16,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:16,186] [INFO] Task started: CheckM
[2024-01-24 14:40:16,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016918855.1_ASM1691885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016918855.1_ASM1691885v1_genomic.fna/checkm_input GCF_016918855.1_ASM1691885v1_genomic.fna/checkm_result
[2024-01-24 14:42:08,023] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:08,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:08,047] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:08,047] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:08,047] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016918855.1_ASM1691885v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:08,048] [INFO] Task started: Blastn
[2024-01-24 14:42:08,048] [INFO] Running command: blastn -query GCF_016918855.1_ASM1691885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg396f9093-9bc1-4368-b0a5-4652f86898ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_016918855.1_ASM1691885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:10,305] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:10,308] [INFO] Selected 16 target genomes.
[2024-01-24 14:42:10,309] [INFO] Target genome list was writen to GCF_016918855.1_ASM1691885v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:10,320] [INFO] Task started: fastANI
[2024-01-24 14:42:10,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0127270-c4c3-44fc-b90b-71bec2fbbaf3/GCF_016918855.1_ASM1691885v1_genomic.fna.gz --refList GCF_016918855.1_ASM1691885v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016918855.1_ASM1691885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:46,231] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:46,244] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:46,245] [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_016918855.1	s__Streptomyces acididurans	100.0	3196	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900103985.1	s__Streptomyces guanduensis	83.5221	1691	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091855.1	s__Streptomyces sp900091855	83.4853	1430	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900110255.1	s__Streptomyces rubidus	83.4221	1711	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	83.1565	1592	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900142575.1	s__Streptomyces paucisporeus	83.1547	1593	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596445.1	s__Streptomyces sp014596445	82.9228	1537	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107965.1	s__Streptomyces yanglinensis	82.879	1741	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	82.8046	1544	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756395.1	s__Streptomyces sp016756395	82.4835	1630	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721495.1	s__Streptomyces sp000721495	82.322	1584	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916255.1	s__Streptomyces mobaraensis	79.7622	1151	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.59	99.19	0.96	0.92	3	-
GCF_014253015.1	s__Streptomyces sp014253015	79.6844	1132	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160875.1	s__Streptomyces chromofuscus	79.6842	1138	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_000721105.1	s__Streptomyces cellulosae_A	79.2154	1247	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	78.944	1272	3198	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:46,246] [INFO] GTDB search result was written to GCF_016918855.1_ASM1691885v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:46,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:46,251] [INFO] DFAST_QC result json was written to GCF_016918855.1_ASM1691885v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:46,252] [INFO] DFAST_QC completed!
[2024-01-24 14:42:46,252] [INFO] Total running time: 0h3m44s