[2023-06-12 23:45:30,452] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:45:30,455] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:45:30,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg84596b16-9400-4ec4-839f-e6b376afeab7/dqc_reference
[2023-06-12 23:45:33,433] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:45:33,434] [INFO] Task started: Prodigal
[2023-06-12 23:45:33,434] [INFO] Running command: gunzip -c /var/lib/cwl/stg368b46de-8d77-4fc7-bffa-94a442e6435a/GCA_022448845.1_ASM2244884v1_genomic.fna.gz | prodigal -d GCA_022448845.1_ASM2244884v1_genomic.fna/cds.fna -a GCA_022448845.1_ASM2244884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:45:38,223] [INFO] Task succeeded: Prodigal
[2023-06-12 23:45:38,224] [INFO] Task started: HMMsearch
[2023-06-12 23:45:38,224] [INFO] Running command: hmmsearch --tblout GCA_022448845.1_ASM2244884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84596b16-9400-4ec4-839f-e6b376afeab7/dqc_reference/reference_markers.hmm GCA_022448845.1_ASM2244884v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:45:38,437] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:45:38,439] [INFO] Found 6/6 markers.
[2023-06-12 23:45:38,470] [INFO] Query marker FASTA was written to GCA_022448845.1_ASM2244884v1_genomic.fna/markers.fasta
[2023-06-12 23:45:38,471] [INFO] Task started: Blastn
[2023-06-12 23:45:38,471] [INFO] Running command: blastn -query GCA_022448845.1_ASM2244884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84596b16-9400-4ec4-839f-e6b376afeab7/dqc_reference/reference_markers.fasta -out GCA_022448845.1_ASM2244884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:45:39,269] [INFO] Task succeeded: Blastn
[2023-06-12 23:45:39,274] [INFO] Selected 31 target genomes.
[2023-06-12 23:45:39,275] [INFO] Target genome list was writen to GCA_022448845.1_ASM2244884v1_genomic.fna/target_genomes.txt
[2023-06-12 23:45:39,284] [INFO] Task started: fastANI
[2023-06-12 23:45:39,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg368b46de-8d77-4fc7-bffa-94a442e6435a/GCA_022448845.1_ASM2244884v1_genomic.fna.gz --refList GCA_022448845.1_ASM2244884v1_genomic.fna/target_genomes.txt --output GCA_022448845.1_ASM2244884v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:46:02,376] [INFO] Task succeeded: fastANI
[2023-06-12 23:46:02,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84596b16-9400-4ec4-839f-e6b376afeab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:46:02,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84596b16-9400-4ec4-839f-e6b376afeab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:46:02,400] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:46:02,401] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:46:02,401] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.9254	106	467	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.5827	102	467	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.5394	93	467	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.525	91	467	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.4973	82	467	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.4973	82	467	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	76.4413	61	467	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.4375	65	467	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	76.4029	67	467	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.3728	85	467	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.3643	82	467	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.3578	81	467	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.3184	51	467	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.315	87	467	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.2907	106	467	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.2875	107	467	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.2547	108	467	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	76.2298	53	467	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.1999	106	467	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.1891	54	467	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.1004	76	467	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.0945	51	467	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.0696	78	467	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	76.0602	61	467	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.9617	79	467	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.8715	67	467	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.8666	62	467	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.8568	73	467	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	75.7846	80	467	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:46:02,404] [INFO] DFAST Taxonomy check result was written to GCA_022448845.1_ASM2244884v1_genomic.fna/tc_result.tsv
[2023-06-12 23:46:02,405] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:46:02,405] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:46:02,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84596b16-9400-4ec4-839f-e6b376afeab7/dqc_reference/checkm_data
[2023-06-12 23:46:02,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:46:02,431] [INFO] Task started: CheckM
[2023-06-12 23:46:02,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448845.1_ASM2244884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448845.1_ASM2244884v1_genomic.fna/checkm_input GCA_022448845.1_ASM2244884v1_genomic.fna/checkm_result
[2023-06-12 23:46:22,799] [INFO] Task succeeded: CheckM
[2023-06-12 23:46:22,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:46:22,825] [INFO] ===== Completeness check finished =====
[2023-06-12 23:46:22,826] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:46:22,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448845.1_ASM2244884v1_genomic.fna/markers.fasta)
[2023-06-12 23:46:22,826] [INFO] Task started: Blastn
[2023-06-12 23:46:22,827] [INFO] Running command: blastn -query GCA_022448845.1_ASM2244884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84596b16-9400-4ec4-839f-e6b376afeab7/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448845.1_ASM2244884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:46:24,280] [INFO] Task succeeded: Blastn
[2023-06-12 23:46:24,284] [INFO] Selected 13 target genomes.
[2023-06-12 23:46:24,285] [INFO] Target genome list was writen to GCA_022448845.1_ASM2244884v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:46:24,301] [INFO] Task started: fastANI
[2023-06-12 23:46:24,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg368b46de-8d77-4fc7-bffa-94a442e6435a/GCA_022448845.1_ASM2244884v1_genomic.fna.gz --refList GCA_022448845.1_ASM2244884v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448845.1_ASM2244884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:46:30,679] [INFO] Task succeeded: fastANI
[2023-06-12 23:46:30,692] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:46:30,692] [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_002938075.1	s__Casp-alpha2 sp002938075	98.2129	349	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	conclusive
GCA_002686255.1	s__Casp-alpha2 sp002686255	91.3128	372	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_016763915.1	s__Casp-alpha2 sp016763915	79.7898	155	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	78.5195	247	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_016187325.1	s__JACPJY01 sp016187325	78.4776	228	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	78.4735	163	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203955.1	s__Casp-alpha2 sp013203955	78.4699	254	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938315.1	s__Casp-alpha2 sp002938315	78.2274	207	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	77.4863	168	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	77.0873	146	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_009694195.1	s__SHVQ01 sp009694195	76.4438	63	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__SHVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	76.1004	76	467	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:46:30,694] [INFO] GTDB search result was written to GCA_022448845.1_ASM2244884v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:46:30,694] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:46:30,699] [INFO] DFAST_QC result json was written to GCA_022448845.1_ASM2244884v1_genomic.fna/dqc_result.json
[2023-06-12 23:46:30,699] [INFO] DFAST_QC completed!
[2023-06-12 23:46:30,699] [INFO] Total running time: 0h1m0s