[2023-03-18 10:12:10,237] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:12:10,237] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:12:10,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg5281e410-84be-48dc-9f26-1417d3cd5e08/dqc_reference
[2023-03-18 10:12:11,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:12:11,351] [INFO] Task started: Prodigal
[2023-03-18 10:12:11,351] [INFO] Running command: cat /var/lib/cwl/stg4aa848ca-b3cb-45cd-8495-4a3b3faefc52/OceanDNA-b30782.fa | prodigal -d OceanDNA-b30782/cds.fna -a OceanDNA-b30782/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:12:24,116] [INFO] Task succeeded: Prodigal
[2023-03-18 10:12:24,116] [INFO] Task started: HMMsearch
[2023-03-18 10:12:24,116] [INFO] Running command: hmmsearch --tblout OceanDNA-b30782/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5281e410-84be-48dc-9f26-1417d3cd5e08/dqc_reference/reference_markers.hmm OceanDNA-b30782/protein.faa > /dev/null
[2023-03-18 10:12:24,287] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:12:24,288] [INFO] Found 6/6 markers.
[2023-03-18 10:12:24,303] [INFO] Query marker FASTA was written to OceanDNA-b30782/markers.fasta
[2023-03-18 10:12:24,304] [INFO] Task started: Blastn
[2023-03-18 10:12:24,304] [INFO] Running command: blastn -query OceanDNA-b30782/markers.fasta -db /var/lib/cwl/stg5281e410-84be-48dc-9f26-1417d3cd5e08/dqc_reference/reference_markers.fasta -out OceanDNA-b30782/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:24,969] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:25,072] [INFO] Selected 30 target genomes.
[2023-03-18 10:12:25,072] [INFO] Target genome list was writen to OceanDNA-b30782/target_genomes.txt
[2023-03-18 10:12:25,116] [INFO] Task started: fastANI
[2023-03-18 10:12:25,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa848ca-b3cb-45cd-8495-4a3b3faefc52/OceanDNA-b30782.fa --refList OceanDNA-b30782/target_genomes.txt --output OceanDNA-b30782/fastani_result.tsv --threads 1
[2023-03-18 10:12:46,203] [INFO] Task succeeded: fastANI
[2023-03-18 10:12:46,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5281e410-84be-48dc-9f26-1417d3cd5e08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:12:46,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5281e410-84be-48dc-9f26-1417d3cd5e08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:12:46,214] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:12:46,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:12:46,214] [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
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.473	64	686	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.2199	90	686	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.171	82	686	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.1046	90	686	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.0871	85	686	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.9714	78	686	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.9428	82	686	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.9395	78	686	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.8761	84	686	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.8041	81	686	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.749	87	686	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.7406	78	686	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.7252	91	686	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.6405	86	686	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.6402	86	686	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	75.6394	88	686	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.6351	55	686	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.2979	68	686	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:12:46,215] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30782/tc_result.tsv
[2023-03-18 10:12:46,215] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:12:46,215] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:12:46,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5281e410-84be-48dc-9f26-1417d3cd5e08/dqc_reference/checkm_data
[2023-03-18 10:12:46,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:12:46,251] [INFO] Task started: CheckM
[2023-03-18 10:12:46,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30782/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30782/checkm_input OceanDNA-b30782/checkm_result
[2023-03-18 10:13:21,101] [INFO] Task succeeded: CheckM
[2023-03-18 10:13:21,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:13:21,106] [INFO] ===== Completeness check finished =====
[2023-03-18 10:13:21,107] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:13:21,107] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30782/markers.fasta)
[2023-03-18 10:13:21,108] [INFO] Task started: Blastn
[2023-03-18 10:13:21,108] [INFO] Running command: blastn -query OceanDNA-b30782/markers.fasta -db /var/lib/cwl/stg5281e410-84be-48dc-9f26-1417d3cd5e08/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30782/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:13:22,289] [INFO] Task succeeded: Blastn
[2023-03-18 10:13:22,292] [INFO] Selected 22 target genomes.
[2023-03-18 10:13:22,292] [INFO] Target genome list was writen to OceanDNA-b30782/target_genomes_gtdb.txt
[2023-03-18 10:13:22,425] [INFO] Task started: fastANI
[2023-03-18 10:13:22,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa848ca-b3cb-45cd-8495-4a3b3faefc52/OceanDNA-b30782.fa --refList OceanDNA-b30782/target_genomes_gtdb.txt --output OceanDNA-b30782/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:13:33,691] [INFO] Task succeeded: fastANI
[2023-03-18 10:13:33,702] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:13:33,702] [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	80.2974	315	686	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_002686255.1	s__Casp-alpha2 sp002686255	79.9843	386	686	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_002938315.1	s__Casp-alpha2 sp002938315	78.1563	235	686	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_016763915.1	s__Casp-alpha2 sp016763915	77.9296	168	686	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_016187325.1	s__JACPJY01 sp016187325	77.6425	227	686	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	77.3996	167	686	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	77.3636	240	686	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_013204265.1	s__Casp-alpha2 sp013204265	76.9838	140	686	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_001830425.1	s__2-02-FULL-58-16 sp001830425	76.6411	78	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16	95.0	99.96	99.96	0.97	0.97	2	-
GCA_013349695.1	s__GCA-2686765 sp013349695	76.5362	98	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__GCA-2686765	95.0	98.27	95.45	0.83	0.65	4	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.4655	99	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	76.4082	111	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCA_009693905.1	s__2-12-FULL-67-15 sp009693905	76.3166	90	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	99.79	99.79	0.72	0.72	2	-
GCA_017644185.1	s__UBA4479 sp017644185	76.1556	62	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	76.14	59	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018662005.1	s__JACNJU01 sp018662005	75.8333	54	686	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_017418605.1	s__CAISGS01 sp017418605	75.7617	60	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968135.1	s__Magnetospira sp000968135	75.7468	52	686	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospiraceae;g__Magnetospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:13:33,703] [INFO] GTDB search result was written to OceanDNA-b30782/result_gtdb.tsv
[2023-03-18 10:13:33,704] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:13:33,708] [INFO] DFAST_QC result json was written to OceanDNA-b30782/dqc_result.json
[2023-03-18 10:13:33,708] [INFO] DFAST_QC completed!
[2023-03-18 10:13:33,708] [INFO] Total running time: 0h1m23s