[2024-01-25 19:57:05,532] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:05,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:05,534] [INFO] DQC Reference Directory: /var/lib/cwl/stg39bbfea2-1972-42e7-b885-0066a0bcb8bb/dqc_reference
[2024-01-25 19:57:06,703] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:06,703] [INFO] Task started: Prodigal
[2024-01-25 19:57:06,704] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e7c16dd-6121-4f82-ab5a-e169d48fbea3/GCF_013409065.1_ASM1340906v1_genomic.fna.gz | prodigal -d GCF_013409065.1_ASM1340906v1_genomic.fna/cds.fna -a GCF_013409065.1_ASM1340906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:18,304] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:18,305] [INFO] Task started: HMMsearch
[2024-01-25 19:57:18,305] [INFO] Running command: hmmsearch --tblout GCF_013409065.1_ASM1340906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39bbfea2-1972-42e7-b885-0066a0bcb8bb/dqc_reference/reference_markers.hmm GCF_013409065.1_ASM1340906v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:18,577] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:18,578] [INFO] Found 6/6 markers.
[2024-01-25 19:57:18,613] [INFO] Query marker FASTA was written to GCF_013409065.1_ASM1340906v1_genomic.fna/markers.fasta
[2024-01-25 19:57:18,613] [INFO] Task started: Blastn
[2024-01-25 19:57:18,613] [INFO] Running command: blastn -query GCF_013409065.1_ASM1340906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39bbfea2-1972-42e7-b885-0066a0bcb8bb/dqc_reference/reference_markers.fasta -out GCF_013409065.1_ASM1340906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:19,595] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:19,597] [INFO] Selected 23 target genomes.
[2024-01-25 19:57:19,598] [INFO] Target genome list was writen to GCF_013409065.1_ASM1340906v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:19,640] [INFO] Task started: fastANI
[2024-01-25 19:57:19,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e7c16dd-6121-4f82-ab5a-e169d48fbea3/GCF_013409065.1_ASM1340906v1_genomic.fna.gz --refList GCF_013409065.1_ASM1340906v1_genomic.fna/target_genomes.txt --output GCF_013409065.1_ASM1340906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:36,007] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:36,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39bbfea2-1972-42e7-b885-0066a0bcb8bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:36,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39bbfea2-1972-42e7-b885-0066a0bcb8bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:36,021] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:57:36,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:36,021] [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
Spelaeicoccus albus	strain=DSM 26341	GCA_013409065.1	1280376	1280376	type	True	100.0	1342	1343	95	conclusive
Spelaeicoccus albus	strain=DSM 26341	GCA_021729195.1	1280376	1280376	type	True	99.9493	1276	1343	95	conclusive
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_014639315.1	1774748	1774748	type	True	77.5355	136	1343	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	77.4965	136	1343	95	below_threshold
Brevibacterium luteolum	strain=DSM 15022	GCA_016907415.1	199591	199591	type	True	77.1453	138	1343	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	77.1047	121	1343	95	below_threshold
Brevibacterium casei	strain=FDAARGOS_936	GCA_016026595.1	33889	33889	type	True	76.9815	139	1343	95	below_threshold
Brevibacterium luteolum	strain=CCUG 46604	GCA_013004595.1	199591	199591	type	True	76.7687	139	1343	95	below_threshold
Brevibacterium casei	strain=CIP 102111	GCA_900169275.1	33889	33889	type	True	76.7343	137	1343	95	below_threshold
Ruania halotolerans	strain=M4N3S171	GCA_021049285.1	2897773	2897773	type	True	76.5961	86	1343	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	76.5577	118	1343	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	76.5234	100	1343	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	76.4593	114	1343	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.433	138	1343	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	76.3418	133	1343	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	76.1537	158	1343	95	below_threshold
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	76.1361	121	1343	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	76.0652	139	1343	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.0556	107	1343	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	76.0297	99	1343	95	below_threshold
Streptomyces cacaoi	strain=DSM 40057	GCA_013004455.1	1898	1898	type	True	75.634	143	1343	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	75.5933	135	1343	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	75.5854	152	1343	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:36,022] [INFO] DFAST Taxonomy check result was written to GCF_013409065.1_ASM1340906v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:36,023] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:36,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:36,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39bbfea2-1972-42e7-b885-0066a0bcb8bb/dqc_reference/checkm_data
[2024-01-25 19:57:36,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:36,082] [INFO] Task started: CheckM
[2024-01-25 19:57:36,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409065.1_ASM1340906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409065.1_ASM1340906v1_genomic.fna/checkm_input GCF_013409065.1_ASM1340906v1_genomic.fna/checkm_result
[2024-01-25 19:58:12,652] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:12,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:12,668] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:12,668] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:12,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409065.1_ASM1340906v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:12,669] [INFO] Task started: Blastn
[2024-01-25 19:58:12,669] [INFO] Running command: blastn -query GCF_013409065.1_ASM1340906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39bbfea2-1972-42e7-b885-0066a0bcb8bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409065.1_ASM1340906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:14,060] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:14,063] [INFO] Selected 25 target genomes.
[2024-01-25 19:58:14,063] [INFO] Target genome list was writen to GCF_013409065.1_ASM1340906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:14,081] [INFO] Task started: fastANI
[2024-01-25 19:58:14,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e7c16dd-6121-4f82-ab5a-e169d48fbea3/GCF_013409065.1_ASM1340906v1_genomic.fna.gz --refList GCF_013409065.1_ASM1340906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409065.1_ASM1340906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:31,014] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:31,028] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:31,028] [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_013409065.1	s__Spelaeicoccus albus	100.0	1342	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Spelaeicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014639315.1	s__Sediminivirga luteola	77.4931	138	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Sediminivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280295.1	s__Brevibacterium sp005280295	77.3668	137	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359525.1	s__Brevibacterium luteolum_A	77.0431	129	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.39	96.39	0.93	0.93	2	-
GCF_013004595.1	s__Brevibacterium luteolum	76.7687	139	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.16	95.46	0.92	0.89	7	-
GCF_900169275.1	s__Brevibacterium casei	76.7343	137	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.23	97.33	0.93	0.90	17	-
GCF_004135345.1	s__Xylanimonas allomyrinae	76.7211	136	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315415.1	s__Brevibacterium celere_A	76.7116	144	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	76.6327	148	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396155.1	s__Cellulomonas septica	76.5411	114	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117545.1	s__Brevibacterium intestinavium	76.5388	111	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.71	98.71	0.97	0.97	2	-
GCF_002563715.1	s__Isoptericola jiangsuensis	76.4981	166	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421225.1	s__Ruania albidiflava	76.4593	114	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Ruania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001968825.1	s__Tersicoccus sp001968825	76.4543	153	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643255.1	s__Tersicoccus solisilvae	76.4365	154	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	76.4219	157	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_009846865.1	s__Xylanimonas puerhi	76.3937	161	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999765.1	s__Sinomonas mesophila	76.3292	134	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	76.2889	156	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679345.1	s__Cellulomonas cellulans_A	76.1287	171	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024345.1	s__Kribbella flavida	76.0814	155	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250645.1	s__Motilibacter_A aurantiacus	76.0699	106	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	76.0292	144	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	75.9556	117	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539165.1	s__Streptomyces cacaoi	75.6002	150	1343	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.44	99.09	0.96	0.94	7	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:31,030] [INFO] GTDB search result was written to GCF_013409065.1_ASM1340906v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:31,030] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:31,033] [INFO] DFAST_QC result json was written to GCF_013409065.1_ASM1340906v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:31,034] [INFO] DFAST_QC completed!
[2024-01-25 19:58:31,034] [INFO] Total running time: 0h1m26s