[2024-01-24 13:18:41,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,209] [INFO] DQC Reference Directory: /var/lib/cwl/stge9c97299-1a22-4ba8-adf7-7d8d8467f134/dqc_reference
[2024-01-24 13:18:42,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,412] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,412] [INFO] Running command: gunzip -c /var/lib/cwl/stg54d9acbe-f100-4a67-842c-b54144b867ea/GCF_007827045.1_ASM782704v1_genomic.fna.gz | prodigal -d GCF_007827045.1_ASM782704v1_genomic.fna/cds.fna -a GCF_007827045.1_ASM782704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:07,953] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:07,954] [INFO] Task started: HMMsearch
[2024-01-24 13:19:07,954] [INFO] Running command: hmmsearch --tblout GCF_007827045.1_ASM782704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9c97299-1a22-4ba8-adf7-7d8d8467f134/dqc_reference/reference_markers.hmm GCF_007827045.1_ASM782704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:08,325] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:08,327] [INFO] Found 6/6 markers.
[2024-01-24 13:19:08,397] [INFO] Query marker FASTA was written to GCF_007827045.1_ASM782704v1_genomic.fna/markers.fasta
[2024-01-24 13:19:08,398] [INFO] Task started: Blastn
[2024-01-24 13:19:08,398] [INFO] Running command: blastn -query GCF_007827045.1_ASM782704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c97299-1a22-4ba8-adf7-7d8d8467f134/dqc_reference/reference_markers.fasta -out GCF_007827045.1_ASM782704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:09,553] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:09,558] [INFO] Selected 28 target genomes.
[2024-01-24 13:19:09,558] [INFO] Target genome list was writen to GCF_007827045.1_ASM782704v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:09,604] [INFO] Task started: fastANI
[2024-01-24 13:19:09,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg54d9acbe-f100-4a67-842c-b54144b867ea/GCF_007827045.1_ASM782704v1_genomic.fna.gz --refList GCF_007827045.1_ASM782704v1_genomic.fna/target_genomes.txt --output GCF_007827045.1_ASM782704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:51,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:51,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9c97299-1a22-4ba8-adf7-7d8d8467f134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:51,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9c97299-1a22-4ba8-adf7-7d8d8467f134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:51,686] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:51,687] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:51,687] [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
Trebonia kvetii	strain=15TR583	GCA_007827045.1	2480626	2480626	type	True	100.0	3067	3067	95	conclusive
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	76.8007	639	3067	95	below_threshold
Actinomadura rubrobrunea	strain=NBRC 15275	GCA_001552235.1	115335	115335	type	True	76.7444	606	3067	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	76.7417	638	3067	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	76.7383	636	3067	95	below_threshold
Actinoallomurus bryophytorum	strain=DSM 102200	GCA_006716425.1	1490222	1490222	type	True	76.6837	650	3067	95	below_threshold
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	76.6084	681	3067	95	below_threshold
Thermomonospora umbrina	strain=DSM 43927	GCA_003386555.1	111806	111806	type	True	76.5691	583	3067	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	76.5576	638	3067	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	76.5469	602	3067	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	76.5286	724	3067	95	below_threshold
Actinomadura oligospora	strain=ATCC 43269	GCA_000518265.1	111804	111804	type	True	76.49	666	3067	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	76.4852	794	3067	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.4152	754	3067	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	76.4061	638	3067	95	below_threshold
Sphaerisporangium rubeum	strain=DSM 44936	GCA_014207705.1	321317	321317	type	True	76.4051	599	3067	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	76.3984	718	3067	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	76.3979	621	3067	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	76.3856	712	3067	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	76.337	532	3067	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	76.2993	677	3067	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	76.193	705	3067	95	below_threshold
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	76.136	318	3067	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	75.8928	645	3067	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	75.7618	323	3067	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	75.7175	837	3067	95	below_threshold
Cellulomonas cellasea	strain=NBRC 3753	GCA_006538745.1	43670	43670	type	True	75.7119	408	3067	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	75.6931	826	3067	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:51,689] [INFO] DFAST Taxonomy check result was written to GCF_007827045.1_ASM782704v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:51,689] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:51,689] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:51,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9c97299-1a22-4ba8-adf7-7d8d8467f134/dqc_reference/checkm_data
[2024-01-24 13:19:51,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:51,772] [INFO] Task started: CheckM
[2024-01-24 13:19:51,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007827045.1_ASM782704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007827045.1_ASM782704v1_genomic.fna/checkm_input GCF_007827045.1_ASM782704v1_genomic.fna/checkm_result
[2024-01-24 13:21:00,377] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:00,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:00,410] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:00,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:00,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007827045.1_ASM782704v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:00,411] [INFO] Task started: Blastn
[2024-01-24 13:21:00,411] [INFO] Running command: blastn -query GCF_007827045.1_ASM782704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9c97299-1a22-4ba8-adf7-7d8d8467f134/dqc_reference/reference_markers_gtdb.fasta -out GCF_007827045.1_ASM782704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:02,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:02,177] [INFO] Selected 17 target genomes.
[2024-01-24 13:21:02,177] [INFO] Target genome list was writen to GCF_007827045.1_ASM782704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:02,289] [INFO] Task started: fastANI
[2024-01-24 13:21:02,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg54d9acbe-f100-4a67-842c-b54144b867ea/GCF_007827045.1_ASM782704v1_genomic.fna.gz --refList GCF_007827045.1_ASM782704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007827045.1_ASM782704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:23,006] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:23,021] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:23,022] [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_007827045.1	s__Trebonia kvetii	100.0	3067	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Trebonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017354375.1	s__Trebonia sp017354375	79.0505	714	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Trebonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239975.1	s__JAFAZE01 sp019239975	78.662	873	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__JAFAZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009784565.1	s__Trebonia sp009784565	78.239	741	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Trebonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140115.1	s__Palsa-504 sp003140115	78.0747	779	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Palsa-504	95.0	99.54	99.54	0.87	0.87	2	-
GCA_019246795.1	s__Palsa-504 sp019246795	78.0329	592	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Palsa-504	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240215.1	s__Bog-532 sp019240215	77.9104	568	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bog-532	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164955.1	s__Bog-532 sp003164955	77.6782	694	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Bog-532	95.0	99.74	99.72	0.91	0.90	3	-
GCA_019245115.1	s__JAFARZ01 sp019245115	77.6377	805	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__JAFARZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003168295.1	s__Palsa-504 sp003168295	77.6293	778	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Palsa-504	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161205.1	s__Palsa-504 sp003161205	77.3682	539	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Palsa-504	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003541285.1	s__UBA9676 sp003541285	77.0112	443	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__UBA9676	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207705.1	s__Sphaerisporangium rubeum	76.4039	600	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003470205.1	s__Cellulomonas rhizosphaerae	76.1666	312	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003755175.1	s__Cellulomonas sp003755175	76.1084	328	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001429255.1	s__Cellulomonas sp001429255	75.9249	356	3067	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCA_019241635.1	s__Palsa-465 sp019241635	75.2955	219	3067	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:23,023] [INFO] GTDB search result was written to GCF_007827045.1_ASM782704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:23,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:23,028] [INFO] DFAST_QC result json was written to GCF_007827045.1_ASM782704v1_genomic.fna/dqc_result.json
[2024-01-24 13:21:23,028] [INFO] DFAST_QC completed!
[2024-01-24 13:21:23,028] [INFO] Total running time: 0h2m42s