[2024-01-24 13:33:40,798] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:40,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:40,800] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7d6f21a-d22d-4a20-833d-8c1c5db224fa/dqc_reference
[2024-01-24 13:33:42,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,001] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg67b026bb-a690-4968-8f76-56a4d47ede16/GCF_002797855.1_ASM279785v1_genomic.fna.gz | prodigal -d GCF_002797855.1_ASM279785v1_genomic.fna/cds.fna -a GCF_002797855.1_ASM279785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:52,917] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:52,918] [INFO] Task started: HMMsearch
[2024-01-24 13:33:52,918] [INFO] Running command: hmmsearch --tblout GCF_002797855.1_ASM279785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7d6f21a-d22d-4a20-833d-8c1c5db224fa/dqc_reference/reference_markers.hmm GCF_002797855.1_ASM279785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:53,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:53,182] [INFO] Found 6/6 markers.
[2024-01-24 13:33:53,217] [INFO] Query marker FASTA was written to GCF_002797855.1_ASM279785v1_genomic.fna/markers.fasta
[2024-01-24 13:33:53,217] [INFO] Task started: Blastn
[2024-01-24 13:33:53,217] [INFO] Running command: blastn -query GCF_002797855.1_ASM279785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7d6f21a-d22d-4a20-833d-8c1c5db224fa/dqc_reference/reference_markers.fasta -out GCF_002797855.1_ASM279785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:54,515] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:54,518] [INFO] Selected 26 target genomes.
[2024-01-24 13:33:54,519] [INFO] Target genome list was writen to GCF_002797855.1_ASM279785v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:54,646] [INFO] Task started: fastANI
[2024-01-24 13:33:54,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b026bb-a690-4968-8f76-56a4d47ede16/GCF_002797855.1_ASM279785v1_genomic.fna.gz --refList GCF_002797855.1_ASM279785v1_genomic.fna/target_genomes.txt --output GCF_002797855.1_ASM279785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:11,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:11,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7d6f21a-d22d-4a20-833d-8c1c5db224fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:11,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7d6f21a-d22d-4a20-833d-8c1c5db224fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:11,691] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:34:11,691] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:34:11,691] [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
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	80.2104	388	1289	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	80.1118	530	1289	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	80.0744	521	1289	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	79.9912	530	1289	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	79.877	539	1289	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	79.8541	486	1289	95	below_threshold
Leifsonia naganoensis	strain=DSM 15166	GCA_013410615.1	150025	150025	type	True	79.8521	522	1289	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	79.8308	503	1289	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.7982	343	1289	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	79.7732	528	1289	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.6952	426	1289	95	below_threshold
Leifsonia shinshuensis	strain=DSM 15165	GCA_013410375.1	150026	150026	type	True	79.6179	499	1289	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.5709	440	1289	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	79.5654	543	1289	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	79.553	444	1289	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.5012	447	1289	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	79.4567	497	1289	95	below_threshold
Cryobacterium psychrotolerans	strain=CGMCC 1.5382	GCA_900101115.1	386301	386301	type	True	79.4352	429	1289	95	below_threshold
Leifsonia soli	strain=DSM 23871	GCA_013408745.1	582665	582665	type	True	79.4165	469	1289	95	below_threshold
Clavibacter michiganensis subsp. michiganensis	strain=LMG 7333	GCA_002240575.1	33013	28447	type	True	79.406	442	1289	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.3981	445	1289	95	below_threshold
Clavibacter michiganensis	strain=VKM Ac-1403	GCA_900168345.1	28447	28447	suspected-type	True	79.3671	439	1289	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	79.3291	468	1289	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	79.3278	462	1289	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	79.1751	403	1289	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	79.1654	399	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:11,696] [INFO] DFAST Taxonomy check result was written to GCF_002797855.1_ASM279785v1_genomic.fna/tc_result.tsv
[2024-01-24 13:34:11,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:11,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:11,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7d6f21a-d22d-4a20-833d-8c1c5db224fa/dqc_reference/checkm_data
[2024-01-24 13:34:11,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:11,742] [INFO] Task started: CheckM
[2024-01-24 13:34:11,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002797855.1_ASM279785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002797855.1_ASM279785v1_genomic.fna/checkm_input GCF_002797855.1_ASM279785v1_genomic.fna/checkm_result
[2024-01-24 13:34:48,684] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:48,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:48,706] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:48,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:48,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002797855.1_ASM279785v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:48,707] [INFO] Task started: Blastn
[2024-01-24 13:34:48,707] [INFO] Running command: blastn -query GCF_002797855.1_ASM279785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7d6f21a-d22d-4a20-833d-8c1c5db224fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_002797855.1_ASM279785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:50,852] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:50,857] [INFO] Selected 27 target genomes.
[2024-01-24 13:34:50,858] [INFO] Target genome list was writen to GCF_002797855.1_ASM279785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:51,053] [INFO] Task started: fastANI
[2024-01-24 13:34:51,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg67b026bb-a690-4968-8f76-56a4d47ede16/GCF_002797855.1_ASM279785v1_genomic.fna.gz --refList GCF_002797855.1_ASM279785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002797855.1_ASM279785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:09,817] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:09,851] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:09,851] [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_002797855.1	s__Compostimonas suwonensis	100.0	1289	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Compostimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013410355.1	s__Agromyces hippuratus	80.1041	530	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576185.1	s__Clavibacter phaseoli	80.0582	322	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.97	95.69	0.87	0.85	4	-
GCA_001725325.1	s__Rhodoglobus sp001725325	79.9655	486	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_005502775.1	s__Herbiconiux sp005502775	79.9197	520	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	99.99	99.99	0.97	0.97	2	-
GCF_014190775.1	s__Leifsonia aquatica	79.7935	526	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.62	97.25	0.95	0.90	3	-
GCA_004297105.1	s__Herbiconiux sp004297105	79.7245	441	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113715.1	s__Herbiconiux sp013113715	79.6245	512	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410375.1	s__Leifsonia shinshuensis	79.6176	499	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002240635.1	s__Clavibacter tessellarius	79.6038	438	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	96.95	95.37	0.96	0.94	3	-
GCF_003384945.1	s__Clavibacter sp003384945	79.5901	435	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664105.1	s__Leifsonia sp003664105	79.5866	487	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627075.1	s__Protaetiibacter intestinalis	79.5635	473	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	79.551	534	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898805.1	s__Leifsonia sp001898805	79.5411	544	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	79.4845	530	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759585.1	s__Frigoribacterium endophyticum	79.4517	453	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.17	96.59	0.92	0.91	6	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	79.4317	435	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013408745.1	s__Leifsonia soli	79.4168	469	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	98.25	98.25	0.89	0.89	2	-
GCF_016907085.1	s__Clavibacter michiganensis_O	79.3818	442	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168345.1	s__Clavibacter michiganensis	79.3408	441	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.05	95.09	0.97	0.88	49	-
GCF_014640535.1	s__Cnuibacter physcomitrellae	79.339	467	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cnuibacter	95.0	98.64	97.29	0.95	0.90	3	-
GCA_005502445.1	s__Yonghaparkia sp005502445	79.2851	396	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801905.1	s__Leifsonia_A flavus	79.2029	426	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000069225.1	s__Clavibacter sepedonicus	79.2023	443	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	99.98	99.98	0.98	0.96	4	-
GCF_010686725.1	s__Galbitalea soli	79.1519	405	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Galbitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010686705.1	s__Diaminobutyricibacter tongyongensis	79.1512	443	1289	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:09,853] [INFO] GTDB search result was written to GCF_002797855.1_ASM279785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:09,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:09,858] [INFO] DFAST_QC result json was written to GCF_002797855.1_ASM279785v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:09,859] [INFO] DFAST_QC completed!
[2024-01-24 13:35:09,859] [INFO] Total running time: 0h1m29s