[2023-03-16 20:45:16,511] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:45:16,511] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:45:16,511] [INFO] DQC Reference Directory: /var/lib/cwl/stga9a22345-c7a5-42a3-a29c-7532120d6500/dqc_reference
[2023-03-16 20:45:17,613] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:45:17,613] [INFO] Task started: Prodigal
[2023-03-16 20:45:17,614] [INFO] Running command: cat /var/lib/cwl/stgb3e196c7-f017-498c-a461-96d83a852731/OceanDNA-b30747.fa | prodigal -d OceanDNA-b30747/cds.fna -a OceanDNA-b30747/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:45:29,682] [INFO] Task succeeded: Prodigal
[2023-03-16 20:45:29,683] [INFO] Task started: HMMsearch
[2023-03-16 20:45:29,683] [INFO] Running command: hmmsearch --tblout OceanDNA-b30747/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9a22345-c7a5-42a3-a29c-7532120d6500/dqc_reference/reference_markers.hmm OceanDNA-b30747/protein.faa > /dev/null
[2023-03-16 20:45:29,847] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:45:29,848] [INFO] Found 6/6 markers.
[2023-03-16 20:45:29,861] [INFO] Query marker FASTA was written to OceanDNA-b30747/markers.fasta
[2023-03-16 20:45:29,862] [INFO] Task started: Blastn
[2023-03-16 20:45:29,862] [INFO] Running command: blastn -query OceanDNA-b30747/markers.fasta -db /var/lib/cwl/stga9a22345-c7a5-42a3-a29c-7532120d6500/dqc_reference/reference_markers.fasta -out OceanDNA-b30747/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:45:30,577] [INFO] Task succeeded: Blastn
[2023-03-16 20:45:30,578] [INFO] Selected 32 target genomes.
[2023-03-16 20:45:30,578] [INFO] Target genome list was writen to OceanDNA-b30747/target_genomes.txt
[2023-03-16 20:45:30,598] [INFO] Task started: fastANI
[2023-03-16 20:45:30,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3e196c7-f017-498c-a461-96d83a852731/OceanDNA-b30747.fa --refList OceanDNA-b30747/target_genomes.txt --output OceanDNA-b30747/fastani_result.tsv --threads 1
[2023-03-16 20:46:05,232] [INFO] Task succeeded: fastANI
[2023-03-16 20:46:05,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9a22345-c7a5-42a3-a29c-7532120d6500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:46:05,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9a22345-c7a5-42a3-a29c-7532120d6500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:46:05,246] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:46:05,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:46:05,246] [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
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.5878	91	644	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.3762	81	644	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.3655	77	644	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.3357	72	644	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.3324	89	644	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.2785	87	644	95	below_threshold
Varunaivibrio sulfuroxidans	strain=DSM 101688	GCA_004341725.1	1773489	1773489	type	True	76.264	70	644	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.2405	55	644	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.9995	88	644	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.9978	67	644	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.9977	67	644	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.9261	66	644	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.9199	65	644	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.9093	67	644	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.9024	59	644	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.7948	72	644	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	75.6555	76	644	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.5826	86	644	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.504	78	644	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.4587	79	644	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.335	84	644	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	75.3146	57	644	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	75.3091	84	644	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.1349	55	644	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:46:05,246] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30747/tc_result.tsv
[2023-03-16 20:46:05,246] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:46:05,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:46:05,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9a22345-c7a5-42a3-a29c-7532120d6500/dqc_reference/checkm_data
[2023-03-16 20:46:05,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:46:05,251] [INFO] Task started: CheckM
[2023-03-16 20:46:05,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30747/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30747/checkm_input OceanDNA-b30747/checkm_result
[2023-03-16 20:46:48,231] [INFO] Task succeeded: CheckM
[2023-03-16 20:46:48,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:46:48,373] [INFO] ===== Completeness check finished =====
[2023-03-16 20:46:48,373] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:46:48,374] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30747/markers.fasta)
[2023-03-16 20:46:48,375] [INFO] Task started: Blastn
[2023-03-16 20:46:48,375] [INFO] Running command: blastn -query OceanDNA-b30747/markers.fasta -db /var/lib/cwl/stga9a22345-c7a5-42a3-a29c-7532120d6500/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30747/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:46:49,744] [INFO] Task succeeded: Blastn
[2023-03-16 20:46:49,745] [INFO] Selected 18 target genomes.
[2023-03-16 20:46:49,745] [INFO] Target genome list was writen to OceanDNA-b30747/target_genomes_gtdb.txt
[2023-03-16 20:46:49,759] [INFO] Task started: fastANI
[2023-03-16 20:46:49,759] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3e196c7-f017-498c-a461-96d83a852731/OceanDNA-b30747.fa --refList OceanDNA-b30747/target_genomes_gtdb.txt --output OceanDNA-b30747/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:47:00,473] [INFO] Task succeeded: fastANI
[2023-03-16 20:47:00,483] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:47:00,483] [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_013204045.1	s__JABMOQ01 sp013204045	99.177	561	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABMOQ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018671895.1	s__JABHGV01 sp018671895	77.5896	192	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABHGV01	95.0	99.83	99.79	0.94	0.93	6	-
GCA_014382375.1	s__JACNJU01 sp014382375	77.4784	176	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JACNJU01	95.0	99.73	99.73	0.94	0.94	2	-
GCA_018662005.1	s__JACNJU01 sp018662005	77.289	189	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JACNJU01	95.0	99.95	99.92	0.95	0.94	5	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.1559	122	644	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_002706405.1	s__UBA1479 sp002706405	77.1496	97	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_016776705.1	s__JADHSW01 sp016776705	77.1398	97	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JADHSW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696205.1	s__UBA1479 sp002696205	76.8085	85	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	76.6858	93	644	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	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	76.5565	77	644	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_002781745.1	s__UBA1479 sp002781745	76.5324	95	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.3524	88	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.2767	87	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.2467	92	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365375.1	s__Azospirillum sp008365375	75.8611	70	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	75.7379	62	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354135.1	s__GLO-3 sp003354135	75.6419	65	644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__GLO-3;g__GLO-3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:47:00,483] [INFO] GTDB search result was written to OceanDNA-b30747/result_gtdb.tsv
[2023-03-16 20:47:00,483] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:47:00,486] [INFO] DFAST_QC result json was written to OceanDNA-b30747/dqc_result.json
[2023-03-16 20:47:00,486] [INFO] DFAST_QC completed!
[2023-03-16 20:47:00,486] [INFO] Total running time: 0h1m44s