[2024-01-25 18:50:20,736] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:20,737] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:20,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg111b77cc-1e65-461d-b19c-3b57d639b768/dqc_reference
[2024-01-25 18:50:21,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:21,976] [INFO] Task started: Prodigal
[2024-01-25 18:50:21,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c85aca9-ff58-4685-8a90-dd744931c5ee/GCF_003751265.1_ASM375126v1_genomic.fna.gz | prodigal -d GCF_003751265.1_ASM375126v1_genomic.fna/cds.fna -a GCF_003751265.1_ASM375126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:30,041] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:30,041] [INFO] Task started: HMMsearch
[2024-01-25 18:50:30,041] [INFO] Running command: hmmsearch --tblout GCF_003751265.1_ASM375126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg111b77cc-1e65-461d-b19c-3b57d639b768/dqc_reference/reference_markers.hmm GCF_003751265.1_ASM375126v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:30,245] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:30,247] [INFO] Found 6/6 markers.
[2024-01-25 18:50:30,277] [INFO] Query marker FASTA was written to GCF_003751265.1_ASM375126v1_genomic.fna/markers.fasta
[2024-01-25 18:50:30,278] [INFO] Task started: Blastn
[2024-01-25 18:50:30,278] [INFO] Running command: blastn -query GCF_003751265.1_ASM375126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg111b77cc-1e65-461d-b19c-3b57d639b768/dqc_reference/reference_markers.fasta -out GCF_003751265.1_ASM375126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:31,661] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:31,665] [INFO] Selected 23 target genomes.
[2024-01-25 18:50:31,665] [INFO] Target genome list was writen to GCF_003751265.1_ASM375126v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:31,676] [INFO] Task started: fastANI
[2024-01-25 18:50:31,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c85aca9-ff58-4685-8a90-dd744931c5ee/GCF_003751265.1_ASM375126v1_genomic.fna.gz --refList GCF_003751265.1_ASM375126v1_genomic.fna/target_genomes.txt --output GCF_003751265.1_ASM375126v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:00,338] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:00,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg111b77cc-1e65-461d-b19c-3b57d639b768/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:00,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg111b77cc-1e65-461d-b19c-3b57d639b768/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:00,352] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:00,352] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:00,353] [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
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	100.0	1269	1270	95	conclusive
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	83.2725	653	1270	95	below_threshold
Quadrisphaera setariae	strain=DD2A	GCA_008041935.1	2593304	2593304	type	True	77.6352	622	1270	95	below_threshold
Kineococcus indalonis	strain=T90	GCA_009906395.1	2696566	2696566	type	True	77.6115	461	1270	95	below_threshold
Quadrisphaera granulorum	strain=DSM 44889	GCA_003149145.1	317664	317664	type	True	77.4771	519	1270	95	below_threshold
Quadrisphaera granulorum	strain=DSM 44889	GCA_900218025.1	317664	317664	type	True	77.4359	526	1270	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	77.4002	565	1270	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.3163	492	1270	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	77.288	439	1270	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	77.2636	559	1270	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.242	597	1270	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	77.2229	561	1270	95	below_threshold
Georgenia faecalis	strain=ZLJ0423	GCA_003710105.1	2483799	2483799	type	True	77.1543	527	1270	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	76.9339	486	1270	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.9014	493	1270	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	76.8659	482	1270	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	76.8414	536	1270	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.6723	503	1270	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	76.6637	338	1270	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	76.2006	385	1270	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	75.7765	614	1270	95	below_threshold
Actinomadura syzygii	strain=GKU157	GCA_008085905.1	1427538	1427538	type	True	75.6507	604	1270	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	75.6128	600	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:00,354] [INFO] DFAST Taxonomy check result was written to GCF_003751265.1_ASM375126v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:00,354] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:00,354] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:00,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg111b77cc-1e65-461d-b19c-3b57d639b768/dqc_reference/checkm_data
[2024-01-25 18:51:00,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:00,394] [INFO] Task started: CheckM
[2024-01-25 18:51:00,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003751265.1_ASM375126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003751265.1_ASM375126v1_genomic.fna/checkm_input GCF_003751265.1_ASM375126v1_genomic.fna/checkm_result
[2024-01-25 18:51:46,375] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:46,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:46,392] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:46,393] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:46,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003751265.1_ASM375126v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:46,393] [INFO] Task started: Blastn
[2024-01-25 18:51:46,393] [INFO] Running command: blastn -query GCF_003751265.1_ASM375126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg111b77cc-1e65-461d-b19c-3b57d639b768/dqc_reference/reference_markers_gtdb.fasta -out GCF_003751265.1_ASM375126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:48,858] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:48,860] [INFO] Selected 21 target genomes.
[2024-01-25 18:51:48,861] [INFO] Target genome list was writen to GCF_003751265.1_ASM375126v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:48,886] [INFO] Task started: fastANI
[2024-01-25 18:51:48,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c85aca9-ff58-4685-8a90-dd744931c5ee/GCF_003751265.1_ASM375126v1_genomic.fna.gz --refList GCF_003751265.1_ASM375126v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003751265.1_ASM375126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:12,520] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:12,533] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:12,534] [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_003751265.1	s__Pseudokineococcus lusitanus	100.0	1269	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013004605.1	s__Pseudokineococcus marinus	83.1128	666	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101335.1	s__Quadrisphaera sp900101335	78.0702	552	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015390235.1	s__Quadrisphaera sp015390235	77.8561	601	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014270065.1	s__Quadrisphaera sp014270065	77.7444	590	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906315.1	s__Kineococcus vitellinus	77.3824	568	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	77.2541	564	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCA_014763705.1	s__Phycicoccus sp014763705	77.1797	396	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991755.1	s__Cellulomonas aerilata	77.105	494	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000767215.1	s__Actinotalea fermentans	77.0959	366	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017565425.1	s__Actinotalea sp017565425	77.0711	422	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198675.1	s__R-H-3 sp002198675	77.0383	729	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013041615.1	s__Pedococcus sp013041615	76.9846	395	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514545.1	s__Actinotalea sp012514545	76.9719	391	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Actinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	76.8481	491	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216915.1	s__Motilibacter rhizosphaerae	76.8164	541	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	76.7546	521	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250645.1	s__Motilibacter_A aurantiacus	76.6259	513	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023105.1	s__Beutenbergia cavernae	76.4329	518	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Beutenbergia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552135.1	s__Spirillospora chibensis	75.7644	617	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008085905.1	s__Spirillospora syzygii	75.6524	599	1270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	95.88	95.88	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:12,535] [INFO] GTDB search result was written to GCF_003751265.1_ASM375126v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:12,536] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:12,539] [INFO] DFAST_QC result json was written to GCF_003751265.1_ASM375126v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:12,539] [INFO] DFAST_QC completed!
[2024-01-25 18:52:12,540] [INFO] Total running time: 0h1m52s