[2024-01-24 14:39:29,424] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:29,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:29,426] [INFO] DQC Reference Directory: /var/lib/cwl/stgeeae9daf-30c5-41ab-bfdf-8ebcb17b0647/dqc_reference
[2024-01-24 14:39:30,736] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:30,737] [INFO] Task started: Prodigal
[2024-01-24 14:39:30,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg004d6d15-aed8-434e-b149-900dbc36e4a1/GCF_003470205.1_ASM347020v1_genomic.fna.gz | prodigal -d GCF_003470205.1_ASM347020v1_genomic.fna/cds.fna -a GCF_003470205.1_ASM347020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:39,729] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:39,730] [INFO] Task started: HMMsearch
[2024-01-24 14:39:39,730] [INFO] Running command: hmmsearch --tblout GCF_003470205.1_ASM347020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeeae9daf-30c5-41ab-bfdf-8ebcb17b0647/dqc_reference/reference_markers.hmm GCF_003470205.1_ASM347020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:39,982] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:39,983] [INFO] Found 6/6 markers.
[2024-01-24 14:39:40,018] [INFO] Query marker FASTA was written to GCF_003470205.1_ASM347020v1_genomic.fna/markers.fasta
[2024-01-24 14:39:40,018] [INFO] Task started: Blastn
[2024-01-24 14:39:40,018] [INFO] Running command: blastn -query GCF_003470205.1_ASM347020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeeae9daf-30c5-41ab-bfdf-8ebcb17b0647/dqc_reference/reference_markers.fasta -out GCF_003470205.1_ASM347020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:41,405] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:41,410] [INFO] Selected 24 target genomes.
[2024-01-24 14:39:41,411] [INFO] Target genome list was writen to GCF_003470205.1_ASM347020v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:41,417] [INFO] Task started: fastANI
[2024-01-24 14:39:41,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg004d6d15-aed8-434e-b149-900dbc36e4a1/GCF_003470205.1_ASM347020v1_genomic.fna.gz --refList GCF_003470205.1_ASM347020v1_genomic.fna/target_genomes.txt --output GCF_003470205.1_ASM347020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:02,982] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:02,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeeae9daf-30c5-41ab-bfdf-8ebcb17b0647/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:02,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeeae9daf-30c5-41ab-bfdf-8ebcb17b0647/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:03,001] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:03,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:03,002] [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
Cellulomonas rhizosphaerae	strain=NEAU-TCZ24	GCA_003470205.1	2293719	2293719	type	True	100.0	1099	1113	95	conclusive
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	82.2981	657	1113	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	82.2405	679	1113	95	below_threshold
Cellulomonas humilata	strain=ATCC 25174	GCA_013359775.1	144055	144055	type	True	82.2232	702	1113	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	82.1969	693	1113	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	82.1714	719	1113	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	82.1005	703	1113	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	82.0968	707	1113	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	82.0551	654	1113	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	82.0452	718	1113	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	82.0333	708	1113	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	81.8443	665	1113	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	81.3069	628	1113	95	below_threshold
Cellulomonas iranensis	strain=NBRC 101100	GCA_001552375.1	76862	76862	type	True	81.2621	626	1113	95	below_threshold
Cellulomonas cellasea	strain=DSM 20118	GCA_000767135.1	43670	43670	type	True	81.0457	563	1113	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.7898	608	1113	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	79.9098	519	1113	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.882	530	1113	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.7235	583	1113	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.6325	527	1113	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.4134	538	1113	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	77.0055	180	1113	95	below_threshold
Streptomyces caatingaensis	strain=CMAA 1322	GCA_001187435.1	1678637	1678637	type	True	76.6493	331	1113	95	below_threshold
Streptomyces corynorhini	strain=AC230	GCA_003346515.1	2282652	2282652	type	True	76.3809	291	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:03,004] [INFO] DFAST Taxonomy check result was written to GCF_003470205.1_ASM347020v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:03,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:03,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:03,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeeae9daf-30c5-41ab-bfdf-8ebcb17b0647/dqc_reference/checkm_data
[2024-01-24 14:40:03,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:03,055] [INFO] Task started: CheckM
[2024-01-24 14:40:03,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003470205.1_ASM347020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003470205.1_ASM347020v1_genomic.fna/checkm_input GCF_003470205.1_ASM347020v1_genomic.fna/checkm_result
[2024-01-24 14:40:49,544] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:49,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:49,565] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:49,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:49,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003470205.1_ASM347020v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:49,566] [INFO] Task started: Blastn
[2024-01-24 14:40:49,566] [INFO] Running command: blastn -query GCF_003470205.1_ASM347020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeeae9daf-30c5-41ab-bfdf-8ebcb17b0647/dqc_reference/reference_markers_gtdb.fasta -out GCF_003470205.1_ASM347020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:51,817] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:51,825] [INFO] Selected 25 target genomes.
[2024-01-24 14:40:51,825] [INFO] Target genome list was writen to GCF_003470205.1_ASM347020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:51,847] [INFO] Task started: fastANI
[2024-01-24 14:40:51,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg004d6d15-aed8-434e-b149-900dbc36e4a1/GCF_003470205.1_ASM347020v1_genomic.fna.gz --refList GCF_003470205.1_ASM347020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003470205.1_ASM347020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:19,235] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:19,257] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:19,258] [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_003470205.1	s__Cellulomonas rhizosphaerae	100.0	1099	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003755175.1	s__Cellulomonas sp003755175	90.7836	970	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837175.1	s__Cellulomonas sp014837175	84.3605	808	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708885.1	s__Cellulomonas sp000708885	83.7224	694	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004306155.1	s__Cellulomonas biazotea	82.3076	657	1113	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	82.2603	716	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.79	98.79	0.94	0.94	2	-
GCA_017744555.1	s__Cellulomonas sp017744555	82.2559	698	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862675.1	s__Cellulomonas chitinilytica	82.2348	748	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989825.1	s__Cellulomonas persica	82.2223	680	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989805.1	s__Cellulomonas xylanilytica	82.2107	715	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538705.1	s__Cellulomonas uda	82.1377	630	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_001426705.1	s__Cellulomonas sp001426705	82.1148	718	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	82.0293	709	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218545.1	s__Cellulomonas gilvus	82.0281	656	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388465.1	s__Cellulomonas sp018388465	81.8902	667	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_001424195.1	s__Cellulomonas sp001424195	81.8459	717	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312005.1	s__Cellulomonas massiliensis	81.8184	667	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000426185.1	s__Cellulomonas sp000426185	81.2859	657	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552375.1	s__Cellulomonas iranensis	81.2719	625	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.21	97.89	0.91	0.88	6	-
GCF_011603975.1	s__Cellulomonas sp011603975	80.6594	551	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409475.1	s__Cellulomonas hominis_B	80.4047	595	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797595.1	s__Sediminihabitans luteus	79.8596	524	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Sediminihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003614925.1	s__Arthrobacter_G celericrescens	76.9934	181	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565305.1	s__Leifsonia sp017565305	76.9426	300	1113	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	97.25	97.25	0.89	0.89	2	-
GCF_003346515.1	s__Streptomyces corynorhini	76.3615	294	1113	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 14:41:19,260] [INFO] GTDB search result was written to GCF_003470205.1_ASM347020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:19,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:19,267] [INFO] DFAST_QC result json was written to GCF_003470205.1_ASM347020v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:19,267] [INFO] DFAST_QC completed!
[2024-01-24 14:41:19,267] [INFO] Total running time: 0h1m50s