[2023-06-29 06:34:29,980] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:34:30,001] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:34:30,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg67e06703-a2e9-44fc-a908-8c9ee70f4825/dqc_reference
[2023-06-29 06:34:31,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:34:31,407] [INFO] Task started: Prodigal
[2023-06-29 06:34:31,407] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c4e963e-5761-4f8a-828d-eb5d17407126/GCA_020252875.1_ASM2025287v1_genomic.fna.gz | prodigal -d GCA_020252875.1_ASM2025287v1_genomic.fna/cds.fna -a GCA_020252875.1_ASM2025287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:34:41,842] [INFO] Task succeeded: Prodigal
[2023-06-29 06:34:41,843] [INFO] Task started: HMMsearch
[2023-06-29 06:34:41,843] [INFO] Running command: hmmsearch --tblout GCA_020252875.1_ASM2025287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67e06703-a2e9-44fc-a908-8c9ee70f4825/dqc_reference/reference_markers.hmm GCA_020252875.1_ASM2025287v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:34:42,156] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:34:42,157] [INFO] Found 6/6 markers.
[2023-06-29 06:34:42,191] [INFO] Query marker FASTA was written to GCA_020252875.1_ASM2025287v1_genomic.fna/markers.fasta
[2023-06-29 06:34:42,191] [INFO] Task started: Blastn
[2023-06-29 06:34:42,191] [INFO] Running command: blastn -query GCA_020252875.1_ASM2025287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67e06703-a2e9-44fc-a908-8c9ee70f4825/dqc_reference/reference_markers.fasta -out GCA_020252875.1_ASM2025287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:34:43,191] [INFO] Task succeeded: Blastn
[2023-06-29 06:34:43,195] [INFO] Selected 30 target genomes.
[2023-06-29 06:34:43,195] [INFO] Target genome list was writen to GCA_020252875.1_ASM2025287v1_genomic.fna/target_genomes.txt
[2023-06-29 06:34:43,207] [INFO] Task started: fastANI
[2023-06-29 06:34:43,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c4e963e-5761-4f8a-828d-eb5d17407126/GCA_020252875.1_ASM2025287v1_genomic.fna.gz --refList GCA_020252875.1_ASM2025287v1_genomic.fna/target_genomes.txt --output GCA_020252875.1_ASM2025287v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:35:15,433] [INFO] Task succeeded: fastANI
[2023-06-29 06:35:15,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67e06703-a2e9-44fc-a908-8c9ee70f4825/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:35:15,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67e06703-a2e9-44fc-a908-8c9ee70f4825/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:35:15,458] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:35:15,458] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:35:15,458] [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
Rhabdaerophilum calidifontis	strain=SYSU G02060	GCA_008641065.1	2604328	2604328	type	True	79.7321	524	1058	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	77.9376	222	1058	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	77.8127	340	1058	95	below_threshold
Microvirga calopogonii	strain=CCBAU 65841	GCA_003347665.1	2078013	2078013	type	True	77.7855	242	1058	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.7481	316	1058	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	77.7189	354	1058	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	77.7183	360	1058	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	77.6544	241	1058	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.6202	289	1058	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.6032	347	1058	95	below_threshold
Microvirga zambiensis	strain=WSM3693	GCA_016735695.1	1402137	1402137	type	True	77.5423	272	1058	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.4659	225	1058	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.452	260	1058	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	77.4359	256	1058	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	77.4076	244	1058	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.342	249	1058	95	below_threshold
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	77.2514	276	1058	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	77.1927	227	1058	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	77.1867	254	1058	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	77.113	224	1058	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	77.0801	251	1058	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.0156	245	1058	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	77.0117	226	1058	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	77.0068	194	1058	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.9969	208	1058	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	76.9746	244	1058	95	below_threshold
Bradyrhizobium hipponense	strain=aSej3	GCA_008123965.1	2605638	2605638	type	True	76.9402	207	1058	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	76.7931	203	1058	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	76.7879	206	1058	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.9142	154	1058	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:35:15,460] [INFO] DFAST Taxonomy check result was written to GCA_020252875.1_ASM2025287v1_genomic.fna/tc_result.tsv
[2023-06-29 06:35:15,461] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:35:15,461] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:35:15,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67e06703-a2e9-44fc-a908-8c9ee70f4825/dqc_reference/checkm_data
[2023-06-29 06:35:15,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:35:15,501] [INFO] Task started: CheckM
[2023-06-29 06:35:15,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020252875.1_ASM2025287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020252875.1_ASM2025287v1_genomic.fna/checkm_input GCA_020252875.1_ASM2025287v1_genomic.fna/checkm_result
[2023-06-29 06:35:53,280] [INFO] Task succeeded: CheckM
[2023-06-29 06:35:53,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 06:35:53,304] [INFO] ===== Completeness check finished =====
[2023-06-29 06:35:53,305] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:35:53,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020252875.1_ASM2025287v1_genomic.fna/markers.fasta)
[2023-06-29 06:35:53,305] [INFO] Task started: Blastn
[2023-06-29 06:35:53,305] [INFO] Running command: blastn -query GCA_020252875.1_ASM2025287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67e06703-a2e9-44fc-a908-8c9ee70f4825/dqc_reference/reference_markers_gtdb.fasta -out GCA_020252875.1_ASM2025287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:35:55,180] [INFO] Task succeeded: Blastn
[2023-06-29 06:35:55,186] [INFO] Selected 18 target genomes.
[2023-06-29 06:35:55,186] [INFO] Target genome list was writen to GCA_020252875.1_ASM2025287v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:35:55,199] [INFO] Task started: fastANI
[2023-06-29 06:35:55,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c4e963e-5761-4f8a-828d-eb5d17407126/GCA_020252875.1_ASM2025287v1_genomic.fna.gz --refList GCA_020252875.1_ASM2025287v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020252875.1_ASM2025287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:36:11,526] [INFO] Task succeeded: fastANI
[2023-06-29 06:36:11,547] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:36:11,548] [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
GCA_002928875.1	s__Rhabdaerophilum sp002928875	85.7618	730	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302635.1	s__Rhabdaerophilum sp017302635	80.4006	593	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008641065.1	s__Rhabdaerophilum calidifontis	79.7229	525	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773635.1	s__Rhabdaerophilum sp009773635	78.9327	472	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009846685.1	s__Rhabdaerophilum sp009846685	78.7794	440	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256205.1	s__Rhabdaerophilum sp002256205	78.7456	453	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhabdaerophilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347665.1	s__Microvirga calopogonii	77.7583	244	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262405.1	s__Microvirga lotononidis	77.6294	243	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735695.1	s__Microvirga zambiensis	77.5423	272	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	77.4776	245	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390695.1	s__Ancylobacter_B sonchi	77.309	252	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415845.1	s__Rhodopseudomonas palustris_F	77.0882	180	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	97.90	97.49	0.94	0.92	8	-
GCF_014636935.1	s__Alsobacter metallidurans	77.0801	251	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009936375.1	s__Methylosinus sp009936375	76.9748	187	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745215.1	s__Methylosinus sp000745215	76.9656	181	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685825.1	s__Methylosinus sp000685825	76.9541	194	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.04	98.49	0.94	0.91	4	-
GCF_011043735.1	s__Methylobacterium sp011043735	76.937	279	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935205.1	s__Rhodopseudomonas palustris_E	76.7061	174	1058	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 06:36:11,550] [INFO] GTDB search result was written to GCA_020252875.1_ASM2025287v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:36:11,550] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:36:11,555] [INFO] DFAST_QC result json was written to GCA_020252875.1_ASM2025287v1_genomic.fna/dqc_result.json
[2023-06-29 06:36:11,555] [INFO] DFAST_QC completed!
[2023-06-29 06:36:11,555] [INFO] Total running time: 0h1m42s