[2024-01-24 14:23:20,682] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:20,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:20,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c86c7c1-9bcd-41a1-b65a-d91f933c34d3/dqc_reference
[2024-01-24 14:23:22,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:22,039] [INFO] Task started: Prodigal
[2024-01-24 14:23:22,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgf84e3601-5d29-41c8-92eb-c2f7508b17ed/GCF_007829035.1_ASM782903v1_genomic.fna.gz | prodigal -d GCF_007829035.1_ASM782903v1_genomic.fna/cds.fna -a GCF_007829035.1_ASM782903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:35,108] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:35,108] [INFO] Task started: HMMsearch
[2024-01-24 14:23:35,108] [INFO] Running command: hmmsearch --tblout GCF_007829035.1_ASM782903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c86c7c1-9bcd-41a1-b65a-d91f933c34d3/dqc_reference/reference_markers.hmm GCF_007829035.1_ASM782903v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:35,484] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:35,485] [INFO] Found 6/6 markers.
[2024-01-24 14:23:35,527] [INFO] Query marker FASTA was written to GCF_007829035.1_ASM782903v1_genomic.fna/markers.fasta
[2024-01-24 14:23:35,527] [INFO] Task started: Blastn
[2024-01-24 14:23:35,527] [INFO] Running command: blastn -query GCF_007829035.1_ASM782903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c86c7c1-9bcd-41a1-b65a-d91f933c34d3/dqc_reference/reference_markers.fasta -out GCF_007829035.1_ASM782903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:36,799] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:36,803] [INFO] Selected 18 target genomes.
[2024-01-24 14:23:36,803] [INFO] Target genome list was writen to GCF_007829035.1_ASM782903v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:36,809] [INFO] Task started: fastANI
[2024-01-24 14:23:36,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84e3601-5d29-41c8-92eb-c2f7508b17ed/GCF_007829035.1_ASM782903v1_genomic.fna.gz --refList GCF_007829035.1_ASM782903v1_genomic.fna/target_genomes.txt --output GCF_007829035.1_ASM782903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:55,341] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:55,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c86c7c1-9bcd-41a1-b65a-d91f933c34d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:55,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c86c7c1-9bcd-41a1-b65a-d91f933c34d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:55,357] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:55,357] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:55,358] [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
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	80.5858	622	1272	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	80.0157	548	1272	95	below_threshold
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	79.8246	546	1272	95	below_threshold
Flexivirga endophytica	strain=CGMCC 1.15085	GCA_014640635.1	1849103	1849103	type	True	79.7958	550	1272	95	below_threshold
Flexivirga caeni	strain=BO-16	GCA_003724155.1	2294115	2294115	type	True	79.7298	541	1272	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	79.4356	467	1272	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	78.9969	418	1272	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	78.6488	331	1272	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.3977	273	1272	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.2631	297	1272	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	78.125	308	1272	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	78.0772	249	1272	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.9291	241	1272	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.8655	243	1272	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	77.3636	177	1272	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	77.1198	242	1272	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	76.9753	238	1272	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	76.8784	185	1272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:55,359] [INFO] DFAST Taxonomy check result was written to GCF_007829035.1_ASM782903v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:55,360] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:55,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:55,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c86c7c1-9bcd-41a1-b65a-d91f933c34d3/dqc_reference/checkm_data
[2024-01-24 14:23:55,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:55,405] [INFO] Task started: CheckM
[2024-01-24 14:23:55,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007829035.1_ASM782903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007829035.1_ASM782903v1_genomic.fna/checkm_input GCF_007829035.1_ASM782903v1_genomic.fna/checkm_result
[2024-01-24 14:24:50,381] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:50,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.42%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:50,413] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:50,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:50,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007829035.1_ASM782903v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:50,415] [INFO] Task started: Blastn
[2024-01-24 14:24:50,415] [INFO] Running command: blastn -query GCF_007829035.1_ASM782903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c86c7c1-9bcd-41a1-b65a-d91f933c34d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_007829035.1_ASM782903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:52,186] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:52,190] [INFO] Selected 14 target genomes.
[2024-01-24 14:24:52,190] [INFO] Target genome list was writen to GCF_007829035.1_ASM782903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:52,204] [INFO] Task started: fastANI
[2024-01-24 14:24:52,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgf84e3601-5d29-41c8-92eb-c2f7508b17ed/GCF_007829035.1_ASM782903v1_genomic.fna.gz --refList GCF_007829035.1_ASM782903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007829035.1_ASM782903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:03,056] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:03,081] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:03,082] [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_007829035.1	s__Rudaeicoccus suwonensis	100.0	1271	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Rudaeicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013002715.1	s__Flexivirga aerilata	80.6053	620	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190805.1	s__Flexivirga oryzae	79.9951	551	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640635.1	s__Flexivirga endophytica	79.7696	552	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003724155.1	s__Flexivirga caeni	79.7595	538	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386865.1	s__Yimella indica	79.5599	425	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716095.1	s__Barrientosiimonas humi	79.4049	456	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013410455.1	s__Allobranchiibius huperziae	79.2228	435	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	97.04	97.04	0.91	0.91	2	-
GCA_001594145.1	s__Branchiibius sp001594145	79.0998	369	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Branchiibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.9937	341	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190945.1	s__Luteipulveratus mongoliensis	78.9602	416	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.239	299	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_013201035.1	s__Phycicoccus sp013201035	78.237	320	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851725.1	s__Cellulomonas algicola	76.995	195	1272	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:03,083] [INFO] GTDB search result was written to GCF_007829035.1_ASM782903v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:03,084] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:03,088] [INFO] DFAST_QC result json was written to GCF_007829035.1_ASM782903v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:03,089] [INFO] DFAST_QC completed!
[2024-01-24 14:25:03,089] [INFO] Total running time: 0h1m42s