[2023-03-17 08:11:32,507] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg29f1a97f-f732-432c-bd1b-c4da0a830b5d/dqc_reference
[2023-03-17 08:11:33,615] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:33,616] [INFO] Task started: Prodigal
[2023-03-17 08:11:33,616] [INFO] Running command: cat /var/lib/cwl/stg8f0f83cb-c2ac-43ef-b151-e0de04adb7e9/OceanDNA-b31270.fa | prodigal -d OceanDNA-b31270/cds.fna -a OceanDNA-b31270/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:58,717] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:58,717] [INFO] Task started: HMMsearch
[2023-03-17 08:11:58,717] [INFO] Running command: hmmsearch --tblout OceanDNA-b31270/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29f1a97f-f732-432c-bd1b-c4da0a830b5d/dqc_reference/reference_markers.hmm OceanDNA-b31270/protein.faa > /dev/null
[2023-03-17 08:11:58,931] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:58,932] [INFO] Found 6/6 markers.
[2023-03-17 08:11:58,956] [INFO] Query marker FASTA was written to OceanDNA-b31270/markers.fasta
[2023-03-17 08:11:58,956] [INFO] Task started: Blastn
[2023-03-17 08:11:58,956] [INFO] Running command: blastn -query OceanDNA-b31270/markers.fasta -db /var/lib/cwl/stg29f1a97f-f732-432c-bd1b-c4da0a830b5d/dqc_reference/reference_markers.fasta -out OceanDNA-b31270/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:59,690] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:59,691] [INFO] Selected 32 target genomes.
[2023-03-17 08:11:59,691] [INFO] Target genome list was writen to OceanDNA-b31270/target_genomes.txt
[2023-03-17 08:11:59,708] [INFO] Task started: fastANI
[2023-03-17 08:11:59,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f0f83cb-c2ac-43ef-b151-e0de04adb7e9/OceanDNA-b31270.fa --refList OceanDNA-b31270/target_genomes.txt --output OceanDNA-b31270/fastani_result.tsv --threads 1
[2023-03-17 08:12:25,743] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:25,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29f1a97f-f732-432c-bd1b-c4da0a830b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:12:25,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29f1a97f-f732-432c-bd1b-c4da0a830b5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:12:25,755] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:12:25,755] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:12:25,755] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.5858	97	1329	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.4013	101	1329	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.2598	121	1329	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	76.0678	106	1329	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	76.0251	93	1329	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.9933	115	1329	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.9862	90	1329	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	75.9194	100	1329	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.901	119	1329	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.861	112	1329	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	75.853	104	1329	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	75.7934	116	1329	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.773	117	1329	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.7632	113	1329	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	75.7532	126	1329	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.7436	127	1329	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.7287	114	1329	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	75.7178	59	1329	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	75.5134	72	1329	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	75.4668	72	1329	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:12:25,755] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31270/tc_result.tsv
[2023-03-17 08:12:25,755] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:12:25,755] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:12:25,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29f1a97f-f732-432c-bd1b-c4da0a830b5d/dqc_reference/checkm_data
[2023-03-17 08:12:25,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:12:25,776] [INFO] Task started: CheckM
[2023-03-17 08:12:25,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31270/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31270/checkm_input OceanDNA-b31270/checkm_result
[2023-03-17 08:13:27,896] [INFO] Task succeeded: CheckM
[2023-03-17 08:13:27,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:13:27,900] [INFO] ===== Completeness check finished =====
[2023-03-17 08:13:27,900] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:13:27,901] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31270/markers.fasta)
[2023-03-17 08:13:27,901] [INFO] Task started: Blastn
[2023-03-17 08:13:27,902] [INFO] Running command: blastn -query OceanDNA-b31270/markers.fasta -db /var/lib/cwl/stg29f1a97f-f732-432c-bd1b-c4da0a830b5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31270/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:13:29,156] [INFO] Task succeeded: Blastn
[2023-03-17 08:13:29,158] [INFO] Selected 21 target genomes.
[2023-03-17 08:13:29,158] [INFO] Target genome list was writen to OceanDNA-b31270/target_genomes_gtdb.txt
[2023-03-17 08:13:29,569] [INFO] Task started: fastANI
[2023-03-17 08:13:29,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f0f83cb-c2ac-43ef-b151-e0de04adb7e9/OceanDNA-b31270.fa --refList OceanDNA-b31270/target_genomes_gtdb.txt --output OceanDNA-b31270/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:13:43,181] [INFO] Task succeeded: fastANI
[2023-03-17 08:13:43,191] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:13:43,191] [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_017640505.1	s__UBA4479 sp017640505	79.9383	654	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017644185.1	s__UBA4479 sp017644185	79.607	667	1329	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_017857825.1	s__UBA4479 sp017857825	77.3727	220	1329	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_002325375.1	s__UBA1479 sp002325375	77.0045	215	1329	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_002696205.1	s__UBA1479 sp002696205	76.9979	183	1329	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_002706405.1	s__UBA1479 sp002706405	76.6492	188	1329	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_016187325.1	s__JACPJY01 sp016187325	76.5902	115	1329	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_016763915.1	s__Casp-alpha2 sp016763915	76.5332	69	1329	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	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.4924	118	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.2333	95	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389175.1	s__UBA4479 sp002389175	76.0543	110	1329	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_011522725.1	s__UBA8309 sp001627655	76.0262	58	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_018702955.1	s__UBA8079 sp018702955	75.9421	61	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCF_902729435.1	s__Magnetospirillum sp902729435	75.8829	94	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	75.7331	68	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_005844085.1	s__Lichenicoccus roseus	75.5627	63	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	75.4971	74	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242505.1	s__Reyranella sp018242505	75.3999	67	1329	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:13:43,193] [INFO] GTDB search result was written to OceanDNA-b31270/result_gtdb.tsv
[2023-03-17 08:13:43,193] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:13:43,195] [INFO] DFAST_QC result json was written to OceanDNA-b31270/dqc_result.json
[2023-03-17 08:13:43,196] [INFO] DFAST_QC completed!
[2023-03-17 08:13:43,196] [INFO] Total running time: 0h2m11s