[2023-03-19 04:58:34,608] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:58:34,608] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:58:34,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e05e94f-bd9b-4090-94f7-2efea076e887/dqc_reference
[2023-03-19 04:58:36,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:58:36,122] [INFO] Task started: Prodigal
[2023-03-19 04:58:36,123] [INFO] Running command: cat /var/lib/cwl/stgd67b235a-f3bb-48bc-b495-5fed6a8a40f4/OceanDNA-b30994.fa | prodigal -d OceanDNA-b30994/cds.fna -a OceanDNA-b30994/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:59:01,707] [INFO] Task succeeded: Prodigal
[2023-03-19 04:59:01,708] [INFO] Task started: HMMsearch
[2023-03-19 04:59:01,708] [INFO] Running command: hmmsearch --tblout OceanDNA-b30994/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e05e94f-bd9b-4090-94f7-2efea076e887/dqc_reference/reference_markers.hmm OceanDNA-b30994/protein.faa > /dev/null
[2023-03-19 04:59:01,923] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:59:01,924] [INFO] Found 6/6 markers.
[2023-03-19 04:59:01,948] [INFO] Query marker FASTA was written to OceanDNA-b30994/markers.fasta
[2023-03-19 04:59:01,949] [INFO] Task started: Blastn
[2023-03-19 04:59:01,949] [INFO] Running command: blastn -query OceanDNA-b30994/markers.fasta -db /var/lib/cwl/stg2e05e94f-bd9b-4090-94f7-2efea076e887/dqc_reference/reference_markers.fasta -out OceanDNA-b30994/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:59:02,816] [INFO] Task succeeded: Blastn
[2023-03-19 04:59:02,817] [INFO] Selected 28 target genomes.
[2023-03-19 04:59:02,817] [INFO] Target genome list was writen to OceanDNA-b30994/target_genomes.txt
[2023-03-19 04:59:02,833] [INFO] Task started: fastANI
[2023-03-19 04:59:02,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgd67b235a-f3bb-48bc-b495-5fed6a8a40f4/OceanDNA-b30994.fa --refList OceanDNA-b30994/target_genomes.txt --output OceanDNA-b30994/fastani_result.tsv --threads 1
[2023-03-19 04:59:25,915] [INFO] Task succeeded: fastANI
[2023-03-19 04:59:25,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e05e94f-bd9b-4090-94f7-2efea076e887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:59:25,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e05e94f-bd9b-4090-94f7-2efea076e887/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:59:25,932] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:59:25,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:59:25,933] [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	77.0553	221	1313	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	77.0061	193	1313	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.9896	277	1313	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.9208	245	1313	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.7987	216	1313	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.7647	187	1313	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.7223	208	1313	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	76.7039	226	1313	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.6488	236	1313	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.6316	238	1313	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.6126	231	1313	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5797	162	1313	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.5774	213	1313	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	76.4892	194	1313	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.4799	96	1313	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.4347	247	1313	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.421	207	1313	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	76.4205	173	1313	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.3536	241	1313	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.3248	242	1313	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.3051	178	1313	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.2466	172	1313	95	below_threshold
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	76.2137	69	1313	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.1901	162	1313	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.8495	157	1313	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	75.8448	122	1313	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	75.8424	92	1313	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.7652	170	1313	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:59:25,933] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30994/tc_result.tsv
[2023-03-19 04:59:25,934] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:59:25,934] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:59:25,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e05e94f-bd9b-4090-94f7-2efea076e887/dqc_reference/checkm_data
[2023-03-19 04:59:25,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:59:26,009] [INFO] Task started: CheckM
[2023-03-19 04:59:26,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30994/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30994/checkm_input OceanDNA-b30994/checkm_result
[2023-03-19 05:00:28,840] [INFO] Task succeeded: CheckM
[2023-03-19 05:00:28,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:00:29,444] [INFO] ===== Completeness check finished =====
[2023-03-19 05:00:29,444] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:00:29,444] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30994/markers.fasta)
[2023-03-19 05:00:29,446] [INFO] Task started: Blastn
[2023-03-19 05:00:29,446] [INFO] Running command: blastn -query OceanDNA-b30994/markers.fasta -db /var/lib/cwl/stg2e05e94f-bd9b-4090-94f7-2efea076e887/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30994/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:00:31,154] [INFO] Task succeeded: Blastn
[2023-03-19 05:00:31,155] [INFO] Selected 9 target genomes.
[2023-03-19 05:00:31,155] [INFO] Target genome list was writen to OceanDNA-b30994/target_genomes_gtdb.txt
[2023-03-19 05:00:31,161] [INFO] Task started: fastANI
[2023-03-19 05:00:31,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgd67b235a-f3bb-48bc-b495-5fed6a8a40f4/OceanDNA-b30994.fa --refList OceanDNA-b30994/target_genomes_gtdb.txt --output OceanDNA-b30994/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:00:38,362] [INFO] Task succeeded: fastANI
[2023-03-19 05:00:38,368] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:00:38,368] [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_002325375.1	s__UBA1479 sp002325375	99.9946	1304	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	conclusive
GCA_002706405.1	s__UBA1479 sp002706405	89.1863	982	1313	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_002781745.1	s__UBA1479 sp002781745	84.5096	863	1313	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_002696205.1	s__UBA1479 sp002696205	83.0439	800	1313	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_002433335.1	s__UBA1479 sp002433335	81.7295	752	1313	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_017640505.1	s__UBA4479 sp017640505	78.3333	265	1313	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_002686255.1	s__Casp-alpha2 sp002686255	77.5459	243	1313	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_017644185.1	s__UBA4479 sp017644185	77.0969	200	1313	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_015232025.1	s__JADFZP01 sp015232025	76.6651	158	1313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:00:38,368] [INFO] GTDB search result was written to OceanDNA-b30994/result_gtdb.tsv
[2023-03-19 05:00:38,369] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:00:38,371] [INFO] DFAST_QC result json was written to OceanDNA-b30994/dqc_result.json
[2023-03-19 05:00:38,371] [INFO] DFAST_QC completed!
[2023-03-19 05:00:38,371] [INFO] Total running time: 0h2m4s