[2024-01-24 13:32:41,628] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg795b115a-fa0f-432c-948f-a3c41f78e04d/dqc_reference
[2024-01-24 13:32:43,102] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,104] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,105] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc428bae-bbeb-4bf5-9af6-faba50a66bae/GCF_018141545.1_ASM1814154v1_genomic.fna.gz | prodigal -d GCF_018141545.1_ASM1814154v1_genomic.fna/cds.fna -a GCF_018141545.1_ASM1814154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:55,176] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:55,177] [INFO] Task started: HMMsearch
[2024-01-24 13:32:55,177] [INFO] Running command: hmmsearch --tblout GCF_018141545.1_ASM1814154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg795b115a-fa0f-432c-948f-a3c41f78e04d/dqc_reference/reference_markers.hmm GCF_018141545.1_ASM1814154v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:55,527] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:55,529] [INFO] Found 6/6 markers.
[2024-01-24 13:32:55,582] [INFO] Query marker FASTA was written to GCF_018141545.1_ASM1814154v1_genomic.fna/markers.fasta
[2024-01-24 13:32:55,583] [INFO] Task started: Blastn
[2024-01-24 13:32:55,583] [INFO] Running command: blastn -query GCF_018141545.1_ASM1814154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg795b115a-fa0f-432c-948f-a3c41f78e04d/dqc_reference/reference_markers.fasta -out GCF_018141545.1_ASM1814154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:56,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:56,410] [INFO] Selected 27 target genomes.
[2024-01-24 13:32:56,410] [INFO] Target genome list was writen to GCF_018141545.1_ASM1814154v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:56,425] [INFO] Task started: fastANI
[2024-01-24 13:32:56,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc428bae-bbeb-4bf5-9af6-faba50a66bae/GCF_018141545.1_ASM1814154v1_genomic.fna.gz --refList GCF_018141545.1_ASM1814154v1_genomic.fna/target_genomes.txt --output GCF_018141545.1_ASM1814154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:25,122] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:25,123] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg795b115a-fa0f-432c-948f-a3c41f78e04d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:25,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg795b115a-fa0f-432c-948f-a3c41f78e04d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:25,148] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:25,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:25,149] [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
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	100.0	1512	1512	95	conclusive
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	81.357	712	1512	95	below_threshold
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	75.9571	254	1512	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.7686	485	1512	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	75.705	410	1512	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.598	437	1512	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	75.5911	377	1512	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	75.5809	439	1512	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	75.5111	374	1512	95	below_threshold
Mobilicoccus pelagius	strain=NBRC 104925	GCA_000247995.2	746032	746032	type	True	75.3092	236	1512	95	below_threshold
Tessaracoccus coleopterorum	strain=HDW20	GCA_011174705.1	2714950	2714950	type	True	75.2097	150	1512	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	75.1574	347	1512	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	75.142	291	1512	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	75.1316	305	1512	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	75.1291	262	1512	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	75.1172	276	1512	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	75.1164	410	1512	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	75.0915	369	1512	95	below_threshold
Streptomyces griseus	strain=DSM 40236	GCA_900105705.1	1911	1911	type	True	75.077	357	1512	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	75.0583	299	1512	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.0541	187	1512	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.0426	179	1512	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	75.0225	343	1512	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	74.9886	424	1512	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	74.9807	154	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,152] [INFO] DFAST Taxonomy check result was written to GCF_018141545.1_ASM1814154v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:25,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:25,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:25,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg795b115a-fa0f-432c-948f-a3c41f78e04d/dqc_reference/checkm_data
[2024-01-24 13:33:25,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:25,223] [INFO] Task started: CheckM
[2024-01-24 13:33:25,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018141545.1_ASM1814154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018141545.1_ASM1814154v1_genomic.fna/checkm_input GCF_018141545.1_ASM1814154v1_genomic.fna/checkm_result
[2024-01-24 13:34:22,007] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:22,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:22,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:22,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:22,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018141545.1_ASM1814154v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:22,033] [INFO] Task started: Blastn
[2024-01-24 13:34:22,033] [INFO] Running command: blastn -query GCF_018141545.1_ASM1814154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg795b115a-fa0f-432c-948f-a3c41f78e04d/dqc_reference/reference_markers_gtdb.fasta -out GCF_018141545.1_ASM1814154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:23,218] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:23,222] [INFO] Selected 23 target genomes.
[2024-01-24 13:34:23,222] [INFO] Target genome list was writen to GCF_018141545.1_ASM1814154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:23,280] [INFO] Task started: fastANI
[2024-01-24 13:34:23,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc428bae-bbeb-4bf5-9af6-faba50a66bae/GCF_018141545.1_ASM1814154v1_genomic.fna.gz --refList GCF_018141545.1_ASM1814154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018141545.1_ASM1814154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:40,413] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:40,433] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:40,433] [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_018141545.1	s__Miltoncostaea oceani	100.0	1512	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__Miltoncostaea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016463385.1	s__Miltoncostaea sp016463385	81.5275	477	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__Miltoncostaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464995.1	s__Miltoncostaea sp001464995	81.3343	595	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__Miltoncostaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018141525.1	s__Miltoncostaea marina	81.325	716	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__Miltoncostaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853415.1	s__SYFI01 sp017853415	77.9879	224	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969105.1	s__SYFI01 sp018969105	77.7829	223	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870155.1	s__SYFI01 sp016870155	77.7268	230	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464275.1	s__Ga0077560 sp001464275	77.593	392	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__Ga0077560	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866425.1	s__SYFI01 sp903866425	77.1007	143	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788075.1	s__SYFI01 sp005788075	77.0257	153	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__SYFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882545.1	s__Ga0077560 sp017882545	76.8943	194	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Miltoncostaeales;f__Miltoncostaeaceae;g__Ga0077560	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873565.1	s__F1-60-MAGs149 sp903873565	76.0334	208	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	98.96	98.77	0.82	0.80	5	-
GCA_016870485.1	s__F1-60-MAGs149 sp016870485	75.7833	259	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826085.1	s__Nigerium massiliense	75.3931	162	1512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Nigerium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014534295.1	s__JACVRU01 sp014534295	75.251	135	1512	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACVRU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011174705.1	s__Arachnia coleopterorum	75.2048	151	1512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405885.1	s__Arthrobacter_D sp016405885	75.1475	107	1512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899645.1	s__Pseudonocardia sp001899645	75.1211	351	1512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	99.47	99.47	0.91	0.91	2	-
GCF_003937945.1	s__Amycolatopsis eburnea	74.9979	422	1512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531495.1	s__Nonomuraea sp018531495	74.9911	361	1512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720385.1	s__Catellatospora vulcania	74.9895	366	1512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357995.1	s__Arthrobacter_D crusticola	74.9378	136	1512	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853315.1	s__REEB422 sp017853315	74.8465	227	1512	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__REEB422	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:40,435] [INFO] GTDB search result was written to GCF_018141545.1_ASM1814154v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:40,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:40,441] [INFO] DFAST_QC result json was written to GCF_018141545.1_ASM1814154v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:40,441] [INFO] DFAST_QC completed!
[2024-01-24 13:34:40,441] [INFO] Total running time: 0h1m59s