[2023-03-17 04:35:35,462] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:35:35,462] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:35:35,463] [INFO] DQC Reference Directory: /var/lib/cwl/stg11b825e5-ff20-4d0f-8fac-92aefd3acc12/dqc_reference
[2023-03-17 04:35:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:35:36,687] [INFO] Task started: Prodigal
[2023-03-17 04:35:36,688] [INFO] Running command: cat /var/lib/cwl/stg41e277a4-fdb4-4031-b0f4-80076485e9cb/OceanDNA-b1008.fa | prodigal -d OceanDNA-b1008/cds.fna -a OceanDNA-b1008/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:35:49,359] [INFO] Task succeeded: Prodigal
[2023-03-17 04:35:49,359] [INFO] Task started: HMMsearch
[2023-03-17 04:35:49,359] [INFO] Running command: hmmsearch --tblout OceanDNA-b1008/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11b825e5-ff20-4d0f-8fac-92aefd3acc12/dqc_reference/reference_markers.hmm OceanDNA-b1008/protein.faa > /dev/null
[2023-03-17 04:35:49,515] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:35:49,516] [INFO] Found 6/6 markers.
[2023-03-17 04:35:49,530] [INFO] Query marker FASTA was written to OceanDNA-b1008/markers.fasta
[2023-03-17 04:35:49,531] [INFO] Task started: Blastn
[2023-03-17 04:35:49,531] [INFO] Running command: blastn -query OceanDNA-b1008/markers.fasta -db /var/lib/cwl/stg11b825e5-ff20-4d0f-8fac-92aefd3acc12/dqc_reference/reference_markers.fasta -out OceanDNA-b1008/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:35:50,174] [INFO] Task succeeded: Blastn
[2023-03-17 04:35:50,175] [INFO] Selected 27 target genomes.
[2023-03-17 04:35:50,175] [INFO] Target genome list was writen to OceanDNA-b1008/target_genomes.txt
[2023-03-17 04:35:50,187] [INFO] Task started: fastANI
[2023-03-17 04:35:50,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg41e277a4-fdb4-4031-b0f4-80076485e9cb/OceanDNA-b1008.fa --refList OceanDNA-b1008/target_genomes.txt --output OceanDNA-b1008/fastani_result.tsv --threads 1
[2023-03-17 04:36:12,472] [INFO] Task succeeded: fastANI
[2023-03-17 04:36:12,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11b825e5-ff20-4d0f-8fac-92aefd3acc12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:36:12,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11b825e5-ff20-4d0f-8fac-92aefd3acc12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:36:12,485] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:36:12,485] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:36:12,485] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.507	209	675	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.3137	196	675	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.2641	144	675	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.6102	149	675	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.3055	169	675	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	75.881	56	675	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	75.8739	59	675	95	below_threshold
Crossiella equi	strain=DSM 44580	GCA_017876755.1	130796	130796	type	True	75.8082	91	675	95	below_threshold
Crossiella equi	strain=NRRL B-24104	GCA_002155995.1	130796	130796	type	True	75.766	86	675	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	75.6902	117	675	95	below_threshold
Streptomyces californicus	strain=NRRL B-2098	GCA_000717645.1	67351	67351	type	True	75.6228	116	675	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	75.6117	77	675	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	75.5844	103	675	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	75.5161	61	675	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	75.4604	94	675	95	below_threshold
Streptomyces verrucosisporus	strain=CPB1-1	GCA_017114865.1	1695161	1695161	type	True	75.4591	93	675	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	75.4562	95	675	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	75.4318	97	675	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	75.4239	113	675	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	75.3295	115	675	95	below_threshold
Streptomyces milbemycinicus	strain=NRRL 5739	GCA_002154605.1	476552	476552	type	True	75.321	101	675	95	below_threshold
Cellulomonas endophytica	strain=SYSUP0004	GCA_004123805.1	2494735	2494735	type	True	75.2109	76	675	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:36:12,485] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1008/tc_result.tsv
[2023-03-17 04:36:12,485] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:36:12,485] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:36:12,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11b825e5-ff20-4d0f-8fac-92aefd3acc12/dqc_reference/checkm_data
[2023-03-17 04:36:12,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:36:12,489] [INFO] Task started: CheckM
[2023-03-17 04:36:12,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1008/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1008/checkm_input OceanDNA-b1008/checkm_result
[2023-03-17 04:36:47,392] [INFO] Task succeeded: CheckM
[2023-03-17 04:36:47,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:36:47,395] [INFO] ===== Completeness check finished =====
[2023-03-17 04:36:47,395] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:36:47,395] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1008/markers.fasta)
[2023-03-17 04:36:47,395] [INFO] Task started: Blastn
[2023-03-17 04:36:47,395] [INFO] Running command: blastn -query OceanDNA-b1008/markers.fasta -db /var/lib/cwl/stg11b825e5-ff20-4d0f-8fac-92aefd3acc12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1008/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:36:48,363] [INFO] Task succeeded: Blastn
[2023-03-17 04:36:48,363] [INFO] Selected 10 target genomes.
[2023-03-17 04:36:48,364] [INFO] Target genome list was writen to OceanDNA-b1008/target_genomes_gtdb.txt
[2023-03-17 04:36:48,691] [INFO] Task started: fastANI
[2023-03-17 04:36:48,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg41e277a4-fdb4-4031-b0f4-80076485e9cb/OceanDNA-b1008.fa --refList OceanDNA-b1008/target_genomes_gtdb.txt --output OceanDNA-b1008/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:36:53,875] [INFO] Task succeeded: fastANI
[2023-03-17 04:36:53,881] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:36:53,882] [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_002699725.1	s__S20-B6 sp002699725	97.1346	575	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	conclusive
GCA_002329075.1	s__S20-B6 sp002329075	87.6814	564	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
GCA_014381945.1	s__S20-B6 sp014381945	86.4657	581	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346745.1	s__S20-B6 sp002346745	82.9739	486	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_016845305.1	s__UBA9410 sp016845305	79.9706	405	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	78.8929	350	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	77.2825	160	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138855.1	s__Bog-756 sp003138855	76.1429	101	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.82	99.61	0.95	0.93	14	-
GCA_002255565.1	s__RAAP-2 sp002255565	76.098	62	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882995.1	s__Chersky-840 sp017882995	76.0372	65	675	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__Chersky-840	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:36:53,882] [INFO] GTDB search result was written to OceanDNA-b1008/result_gtdb.tsv
[2023-03-17 04:36:53,882] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:36:53,884] [INFO] DFAST_QC result json was written to OceanDNA-b1008/dqc_result.json
[2023-03-17 04:36:53,884] [INFO] DFAST_QC completed!
[2023-03-17 04:36:53,884] [INFO] Total running time: 0h1m18s