[2023-03-15 13:45:07,857] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:45:07,858] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:45:07,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8788284-f4c5-47ee-8f6d-d019bb68dcf3/dqc_reference
[2023-03-15 13:45:09,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:45:09,270] [INFO] Task started: Prodigal
[2023-03-15 13:45:09,270] [INFO] Running command: cat /var/lib/cwl/stga655d359-d91a-4bcf-b31c-e51cfbebf846/OceanDNA-b30791.fa | prodigal -d OceanDNA-b30791/cds.fna -a OceanDNA-b30791/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:45:22,456] [INFO] Task succeeded: Prodigal
[2023-03-15 13:45:22,456] [INFO] Task started: HMMsearch
[2023-03-15 13:45:22,456] [INFO] Running command: hmmsearch --tblout OceanDNA-b30791/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8788284-f4c5-47ee-8f6d-d019bb68dcf3/dqc_reference/reference_markers.hmm OceanDNA-b30791/protein.faa > /dev/null
[2023-03-15 13:45:22,632] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:45:22,633] [INFO] Found 6/6 markers.
[2023-03-15 13:45:22,647] [INFO] Query marker FASTA was written to OceanDNA-b30791/markers.fasta
[2023-03-15 13:45:22,648] [INFO] Task started: Blastn
[2023-03-15 13:45:22,648] [INFO] Running command: blastn -query OceanDNA-b30791/markers.fasta -db /var/lib/cwl/stgc8788284-f4c5-47ee-8f6d-d019bb68dcf3/dqc_reference/reference_markers.fasta -out OceanDNA-b30791/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:23,400] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:23,401] [INFO] Selected 33 target genomes.
[2023-03-15 13:45:23,401] [INFO] Target genome list was writen to OceanDNA-b30791/target_genomes.txt
[2023-03-15 13:45:23,423] [INFO] Task started: fastANI
[2023-03-15 13:45:23,423] [INFO] Running command: fastANI --query /var/lib/cwl/stga655d359-d91a-4bcf-b31c-e51cfbebf846/OceanDNA-b30791.fa --refList OceanDNA-b30791/target_genomes.txt --output OceanDNA-b30791/fastani_result.tsv --threads 1
[2023-03-15 13:45:47,250] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:47,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8788284-f4c5-47ee-8f6d-d019bb68dcf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:45:47,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8788284-f4c5-47ee-8f6d-d019bb68dcf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:45:47,270] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:45:47,270] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:45:47,270] [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	76.7539	152	727	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.684	143	727	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.6461	148	727	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.6079	170	727	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.5612	174	727	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.5308	104	727	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.5054	164	727	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.489	177	727	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.4884	116	727	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.4787	128	727	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.4536	173	727	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.4455	161	727	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	76.3643	137	727	95	below_threshold
Varunaivibrio sulfuroxidans	strain=DSM 101688	GCA_004341725.1	1773489	1773489	type	True	76.3576	93	727	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.3571	138	727	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	76.3271	145	727	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.3215	143	727	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.3097	101	727	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.304	155	727	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.2696	123	727	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.2501	104	727	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	76.2048	81	727	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	76.1912	114	727	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.1284	178	727	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.0901	109	727	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.0544	167	727	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.9973	104	727	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.9516	124	727	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.9423	97	727	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.9194	54	727	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	75.8672	94	727	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	75.6764	72	727	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	75.3587	63	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:45:47,271] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30791/tc_result.tsv
[2023-03-15 13:45:47,271] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:45:47,271] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:45:47,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8788284-f4c5-47ee-8f6d-d019bb68dcf3/dqc_reference/checkm_data
[2023-03-15 13:45:47,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:45:47,381] [INFO] Task started: CheckM
[2023-03-15 13:45:47,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30791/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30791/checkm_input OceanDNA-b30791/checkm_result
[2023-03-15 13:46:22,961] [INFO] Task succeeded: CheckM
[2023-03-15 13:46:22,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:46:22,965] [INFO] ===== Completeness check finished =====
[2023-03-15 13:46:22,965] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:46:22,966] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30791/markers.fasta)
[2023-03-15 13:46:22,967] [INFO] Task started: Blastn
[2023-03-15 13:46:22,967] [INFO] Running command: blastn -query OceanDNA-b30791/markers.fasta -db /var/lib/cwl/stgc8788284-f4c5-47ee-8f6d-d019bb68dcf3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30791/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:46:24,422] [INFO] Task succeeded: Blastn
[2023-03-15 13:46:24,424] [INFO] Selected 13 target genomes.
[2023-03-15 13:46:24,424] [INFO] Target genome list was writen to OceanDNA-b30791/target_genomes_gtdb.txt
[2023-03-15 13:46:24,438] [INFO] Task started: fastANI
[2023-03-15 13:46:24,438] [INFO] Running command: fastANI --query /var/lib/cwl/stga655d359-d91a-4bcf-b31c-e51cfbebf846/OceanDNA-b30791.fa --refList OceanDNA-b30791/target_genomes_gtdb.txt --output OceanDNA-b30791/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:46:31,709] [INFO] Task succeeded: fastANI
[2023-03-15 13:46:31,718] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:46:31,718] [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_002686255.1	s__Casp-alpha2 sp002686255	99.8467	685	727	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	conclusive
GCA_002938075.1	s__Casp-alpha2 sp002938075	91.0563	421	727	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_016763915.1	s__Casp-alpha2 sp016763915	79.4681	210	727	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	79.0464	363	727	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	78.9604	317	727	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_014382345.1	s__Casp-alpha2 sp014382345	78.8365	388	727	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_001510075.1	s__Casp-alpha2 sp001510075	78.6038	246	727	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	78.4593	294	727	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	77.7153	267	727	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	77.3614	227	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCF_902729435.1	s__Magnetospirillum sp902729435	77.1544	172	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	77.137	177	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197795.1	s__Rhodospira goensis	76.3375	139	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:46:31,718] [INFO] GTDB search result was written to OceanDNA-b30791/result_gtdb.tsv
[2023-03-15 13:46:31,719] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:46:31,721] [INFO] DFAST_QC result json was written to OceanDNA-b30791/dqc_result.json
[2023-03-15 13:46:31,721] [INFO] DFAST_QC completed!
[2023-03-15 13:46:31,721] [INFO] Total running time: 0h1m24s