[2023-06-05 03:27:34,242] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:27:34,244] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:27:34,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg56c041fb-cfff-4a1c-9a47-abcf3f84c15f/dqc_reference
[2023-06-05 03:27:35,417] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:27:35,417] [INFO] Task started: Prodigal
[2023-06-05 03:27:35,418] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e276034-8ccb-4f72-bd46-2d45c495a514/GCA_004558035.1_ASM455803v1_genomic.fna.gz | prodigal -d GCA_004558035.1_ASM455803v1_genomic.fna/cds.fna -a GCA_004558035.1_ASM455803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:27:44,953] [INFO] Task succeeded: Prodigal
[2023-06-05 03:27:44,953] [INFO] Task started: HMMsearch
[2023-06-05 03:27:44,953] [INFO] Running command: hmmsearch --tblout GCA_004558035.1_ASM455803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56c041fb-cfff-4a1c-9a47-abcf3f84c15f/dqc_reference/reference_markers.hmm GCA_004558035.1_ASM455803v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:27:45,179] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:27:45,181] [INFO] Found 6/6 markers.
[2023-06-05 03:27:45,204] [INFO] Query marker FASTA was written to GCA_004558035.1_ASM455803v1_genomic.fna/markers.fasta
[2023-06-05 03:27:45,205] [INFO] Task started: Blastn
[2023-06-05 03:27:45,205] [INFO] Running command: blastn -query GCA_004558035.1_ASM455803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56c041fb-cfff-4a1c-9a47-abcf3f84c15f/dqc_reference/reference_markers.fasta -out GCA_004558035.1_ASM455803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:27:45,825] [INFO] Task succeeded: Blastn
[2023-06-05 03:27:45,829] [INFO] Selected 28 target genomes.
[2023-06-05 03:27:45,830] [INFO] Target genome list was writen to GCA_004558035.1_ASM455803v1_genomic.fna/target_genomes.txt
[2023-06-05 03:27:45,835] [INFO] Task started: fastANI
[2023-06-05 03:27:45,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e276034-8ccb-4f72-bd46-2d45c495a514/GCA_004558035.1_ASM455803v1_genomic.fna.gz --refList GCA_004558035.1_ASM455803v1_genomic.fna/target_genomes.txt --output GCA_004558035.1_ASM455803v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:28:02,693] [INFO] Task succeeded: fastANI
[2023-06-05 03:28:02,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56c041fb-cfff-4a1c-9a47-abcf3f84c15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:28:02,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56c041fb-cfff-4a1c-9a47-abcf3f84c15f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:28:02,707] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:28:02,708] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:28:02,708] [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
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.1428	52	691	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.061	76	691	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	75.9931	82	691	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	74.9481	64	691	95	below_threshold
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	74.9081	55	691	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	74.9057	51	691	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	74.8912	102	691	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	74.838	98	691	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	74.8327	60	691	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	74.8166	60	691	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.8121	144	691	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	74.7931	65	691	95	below_threshold
Herbidospora galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	74.6482	62	691	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:28:02,710] [INFO] DFAST Taxonomy check result was written to GCA_004558035.1_ASM455803v1_genomic.fna/tc_result.tsv
[2023-06-05 03:28:02,711] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:28:02,711] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:28:02,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56c041fb-cfff-4a1c-9a47-abcf3f84c15f/dqc_reference/checkm_data
[2023-06-05 03:28:02,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:28:02,742] [INFO] Task started: CheckM
[2023-06-05 03:28:02,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004558035.1_ASM455803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004558035.1_ASM455803v1_genomic.fna/checkm_input GCA_004558035.1_ASM455803v1_genomic.fna/checkm_result
[2023-06-05 03:28:33,472] [INFO] Task succeeded: CheckM
[2023-06-05 03:28:33,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:28:33,500] [INFO] ===== Completeness check finished =====
[2023-06-05 03:28:33,500] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:28:33,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004558035.1_ASM455803v1_genomic.fna/markers.fasta)
[2023-06-05 03:28:33,501] [INFO] Task started: Blastn
[2023-06-05 03:28:33,501] [INFO] Running command: blastn -query GCA_004558035.1_ASM455803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56c041fb-cfff-4a1c-9a47-abcf3f84c15f/dqc_reference/reference_markers_gtdb.fasta -out GCA_004558035.1_ASM455803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:28:34,406] [INFO] Task succeeded: Blastn
[2023-06-05 03:28:34,411] [INFO] Selected 11 target genomes.
[2023-06-05 03:28:34,411] [INFO] Target genome list was writen to GCA_004558035.1_ASM455803v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:28:34,553] [INFO] Task started: fastANI
[2023-06-05 03:28:34,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e276034-8ccb-4f72-bd46-2d45c495a514/GCA_004558035.1_ASM455803v1_genomic.fna.gz --refList GCA_004558035.1_ASM455803v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004558035.1_ASM455803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:28:39,621] [INFO] Task succeeded: fastANI
[2023-06-05 03:28:39,634] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:28:39,634] [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_004558035.1	s__Spyradosoma sp004558035	100.0	686	691	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__Spyradosoma	95.0	98.02	97.70	0.95	0.92	3	conclusive
GCA_018713755.1	s__Spyradosoma merdigallinarum	81.3203	287	691	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__Spyradosoma	95.0	97.06	97.06	0.71	0.71	2	-
GCA_017546455.1	s__Spyradosoma sp017546455	78.9389	290	691	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__Spyradosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935025.1	s__Spyradosoma sp017935025	78.6277	197	691	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__Spyradosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017531845.1	s__Spyradosoma sp017531845	78.4652	171	691	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__Spyradosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017440935.1	s__Spyradosoma sp017440935	78.3112	198	691	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__Spyradosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015061905.1	s__Spyradosoma sp015061905	78.2288	218	691	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__Spyradosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904424815.1	s__Merdousia sp001917305	76.2998	56	691	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.91	98.75	0.96	0.93	5	-
GCF_001636295.1	s__Isoptericola dokdonensis	74.891	58	691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	74.8803	106	691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
--------------------------------------------------------------------------------
[2023-06-05 03:28:39,636] [INFO] GTDB search result was written to GCA_004558035.1_ASM455803v1_genomic.fna/result_gtdb.tsv
[2023-06-05 03:28:39,636] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:28:39,640] [INFO] DFAST_QC result json was written to GCA_004558035.1_ASM455803v1_genomic.fna/dqc_result.json
[2023-06-05 03:28:39,640] [INFO] DFAST_QC completed!
[2023-06-05 03:28:39,640] [INFO] Total running time: 0h1m5s