[2023-03-15 18:12:37,909] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:12:37,910] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:12:37,910] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb92fabf-5e91-4f12-aaed-715d043ab9c3/dqc_reference
[2023-03-15 18:12:39,778] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:12:39,779] [INFO] Task started: Prodigal
[2023-03-15 18:12:39,779] [INFO] Running command: cat /var/lib/cwl/stg89d58254-97e1-4334-a03a-dc8395d8a375/OceanDNA-b31271.fa | prodigal -d OceanDNA-b31271/cds.fna -a OceanDNA-b31271/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:13:07,494] [INFO] Task succeeded: Prodigal
[2023-03-15 18:13:07,495] [INFO] Task started: HMMsearch
[2023-03-15 18:13:07,495] [INFO] Running command: hmmsearch --tblout OceanDNA-b31271/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb92fabf-5e91-4f12-aaed-715d043ab9c3/dqc_reference/reference_markers.hmm OceanDNA-b31271/protein.faa > /dev/null
[2023-03-15 18:13:07,718] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:13:07,718] [INFO] Found 6/6 markers.
[2023-03-15 18:13:07,749] [INFO] Query marker FASTA was written to OceanDNA-b31271/markers.fasta
[2023-03-15 18:13:07,751] [INFO] Task started: Blastn
[2023-03-15 18:13:07,751] [INFO] Running command: blastn -query OceanDNA-b31271/markers.fasta -db /var/lib/cwl/stgcb92fabf-5e91-4f12-aaed-715d043ab9c3/dqc_reference/reference_markers.fasta -out OceanDNA-b31271/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:13:08,569] [INFO] Task succeeded: Blastn
[2023-03-15 18:13:08,570] [INFO] Selected 26 target genomes.
[2023-03-15 18:13:08,570] [INFO] Target genome list was writen to OceanDNA-b31271/target_genomes.txt
[2023-03-15 18:13:08,812] [INFO] Task started: fastANI
[2023-03-15 18:13:08,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg89d58254-97e1-4334-a03a-dc8395d8a375/OceanDNA-b31271.fa --refList OceanDNA-b31271/target_genomes.txt --output OceanDNA-b31271/fastani_result.tsv --threads 1
[2023-03-15 18:13:27,209] [INFO] Task succeeded: fastANI
[2023-03-15 18:13:27,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb92fabf-5e91-4f12-aaed-715d043ab9c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:13:27,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb92fabf-5e91-4f12-aaed-715d043ab9c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:13:27,221] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:13:27,221] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:13:27,221] [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	76.4811	126	1393	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.2778	99	1393	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.0778	102	1393	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.0482	113	1393	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.0386	87	1393	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	76.0198	101	1393	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.9578	87	1393	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.9472	109	1393	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.9391	76	1393	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.9263	89	1393	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.9239	89	1393	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.8881	95	1393	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.8435	93	1393	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.8167	99	1393	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	75.6205	57	1393	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.6192	97	1393	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	75.5151	66	1393	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	75.5151	66	1393	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	75.3505	58	1393	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:13:27,221] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31271/tc_result.tsv
[2023-03-15 18:13:27,222] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:13:27,222] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:13:27,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb92fabf-5e91-4f12-aaed-715d043ab9c3/dqc_reference/checkm_data
[2023-03-15 18:13:27,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:13:27,229] [INFO] Task started: CheckM
[2023-03-15 18:13:27,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31271/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31271/checkm_input OceanDNA-b31271/checkm_result
[2023-03-15 18:14:35,744] [INFO] Task succeeded: CheckM
[2023-03-15 18:14:35,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:14:35,747] [INFO] ===== Completeness check finished =====
[2023-03-15 18:14:35,748] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:14:35,748] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31271/markers.fasta)
[2023-03-15 18:14:35,749] [INFO] Task started: Blastn
[2023-03-15 18:14:35,749] [INFO] Running command: blastn -query OceanDNA-b31271/markers.fasta -db /var/lib/cwl/stgcb92fabf-5e91-4f12-aaed-715d043ab9c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31271/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:14:37,271] [INFO] Task succeeded: Blastn
[2023-03-15 18:14:37,272] [INFO] Selected 20 target genomes.
[2023-03-15 18:14:37,273] [INFO] Target genome list was writen to OceanDNA-b31271/target_genomes_gtdb.txt
[2023-03-15 18:14:37,463] [INFO] Task started: fastANI
[2023-03-15 18:14:37,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg89d58254-97e1-4334-a03a-dc8395d8a375/OceanDNA-b31271.fa --refList OceanDNA-b31271/target_genomes_gtdb.txt --output OceanDNA-b31271/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:14:51,241] [INFO] Task succeeded: fastANI
[2023-03-15 18:14:51,251] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:14:51,251] [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	80.0142	643	1393	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	79.8802	665	1393	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	76.9927	201	1393	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_017857825.1	s__UBA4479 sp017857825	76.9759	230	1393	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_002781745.1	s__UBA1479 sp002781745	76.7497	164	1393	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_002869065.1	s__Rhodobium sp002869065	76.5644	88	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706405.1	s__UBA1479 sp002706405	76.5376	172	1393	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	76.3581	110	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.2805	115	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_002389385.1	s__UBA4479 sp002389385	76.1312	101	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.63	99.57	0.92	0.85	8	-
GCA_018671895.1	s__JABHGV01 sp018671895	75.9983	80	1393	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	-
GCF_014904795.1	s__Nisaea nitritireducens	75.9614	108	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389175.1	s__UBA4479 sp002389175	75.9328	117	1393	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_018665815.1	s__UBA3470 sp018665815	75.8931	86	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA3470	95.0	99.65	99.59	0.93	0.91	9	-
GCF_000968135.1	s__Magnetospira sp000968135	75.7002	67	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospiraceae;g__Magnetospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	75.6118	70	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-15 18:14:51,251] [INFO] GTDB search result was written to OceanDNA-b31271/result_gtdb.tsv
[2023-03-15 18:14:51,251] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:14:51,253] [INFO] DFAST_QC result json was written to OceanDNA-b31271/dqc_result.json
[2023-03-15 18:14:51,254] [INFO] DFAST_QC completed!
[2023-03-15 18:14:51,254] [INFO] Total running time: 0h2m13s