[2023-03-16 23:05:03,825] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,825] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a95df0d-d569-4393-b726-9205c6943128/dqc_reference
[2023-03-16 23:05:05,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stg67f0b1b8-8ab4-4654-a152-300087c08d47/OceanDNA-b2835.fa | prodigal -d OceanDNA-b2835/cds.fna -a OceanDNA-b2835/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:33,311] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:33,312] [INFO] Task started: HMMsearch
[2023-03-16 23:05:33,312] [INFO] Running command: hmmsearch --tblout OceanDNA-b2835/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a95df0d-d569-4393-b726-9205c6943128/dqc_reference/reference_markers.hmm OceanDNA-b2835/protein.faa > /dev/null
[2023-03-16 23:05:33,561] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:33,561] [INFO] Found 6/6 markers.
[2023-03-16 23:05:33,595] [INFO] Query marker FASTA was written to OceanDNA-b2835/markers.fasta
[2023-03-16 23:05:33,595] [INFO] Task started: Blastn
[2023-03-16 23:05:33,596] [INFO] Running command: blastn -query OceanDNA-b2835/markers.fasta -db /var/lib/cwl/stg4a95df0d-d569-4393-b726-9205c6943128/dqc_reference/reference_markers.fasta -out OceanDNA-b2835/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:34,563] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:34,564] [INFO] Selected 26 target genomes.
[2023-03-16 23:05:34,564] [INFO] Target genome list was writen to OceanDNA-b2835/target_genomes.txt
[2023-03-16 23:05:34,577] [INFO] Task started: fastANI
[2023-03-16 23:05:34,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg67f0b1b8-8ab4-4654-a152-300087c08d47/OceanDNA-b2835.fa --refList OceanDNA-b2835/target_genomes.txt --output OceanDNA-b2835/fastani_result.tsv --threads 1
[2023-03-16 23:05:59,851] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:59,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a95df0d-d569-4393-b726-9205c6943128/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:59,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a95df0d-d569-4393-b726-9205c6943128/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:59,866] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 23:05:59,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 23:05:59,866] [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
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	96.5692	1397	1507	95	conclusive
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	88.7174	1302	1507	95	below_threshold
Euzebya tangerina	strain=F10	GCA_003074135.1	591198	591198	type	True	77.9479	454	1507	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	76.1362	256	1507	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.9621	265	1507	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	75.9195	266	1507	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	75.8734	211	1507	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	75.6386	185	1507	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	75.5793	214	1507	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	75.5696	306	1507	95	below_threshold
Nocardioides terrae	strain=CGMCC 1.7056	GCA_900112345.1	574651	574651	type	True	75.5516	215	1507	95	below_threshold
Streptosporangium violaceochromogenes	strain=JCM 3281	GCA_014654615.1	46188	46188	type	True	75.53	203	1507	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.4469	205	1507	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	75.3925	307	1507	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	75.3864	367	1507	95	below_threshold
Ornithinimicrobium avium	strain=AMA3305	GCA_003351765.1	2283195	2283195	type	True	75.3639	205	1507	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	75.3522	184	1507	95	below_threshold
Streptomyces corchorusii	strain=DSM 40340	GCA_001514055.1	1903	1903	type	True	75.3246	288	1507	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	75.3148	178	1507	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	75.2959	304	1507	95	below_threshold
Trebonia kvetii	strain=15TR583	GCA_007827045.1	2480626	2480626	type	True	75.257	214	1507	95	below_threshold
Streptomyces canarius	strain=JCM 4733	GCA_014650735.1	285453	285453	type	True	75.2503	311	1507	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	75.2329	214	1507	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	75.2242	169	1507	95	below_threshold
Nocardia thailandica	strain=NBRC 100428	GCA_000308795.1	257275	257275	type	True	75.2208	259	1507	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:59,984] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2835/tc_result.tsv
[2023-03-16 23:05:59,985] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:59,985] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:59,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a95df0d-d569-4393-b726-9205c6943128/dqc_reference/checkm_data
[2023-03-16 23:05:59,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:06:00,054] [INFO] Task started: CheckM
[2023-03-16 23:06:00,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2835/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2835/checkm_input OceanDNA-b2835/checkm_result
[2023-03-16 23:07:32,832] [INFO] Task succeeded: CheckM
[2023-03-16 23:07:32,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:07:32,836] [INFO] ===== Completeness check finished =====
[2023-03-16 23:07:32,836] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:07:32,837] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2835/markers.fasta)
[2023-03-16 23:07:32,837] [INFO] Task started: Blastn
[2023-03-16 23:07:32,837] [INFO] Running command: blastn -query OceanDNA-b2835/markers.fasta -db /var/lib/cwl/stg4a95df0d-d569-4393-b726-9205c6943128/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2835/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:07:34,383] [INFO] Task succeeded: Blastn
[2023-03-16 23:07:34,384] [INFO] Selected 21 target genomes.
[2023-03-16 23:07:34,384] [INFO] Target genome list was writen to OceanDNA-b2835/target_genomes_gtdb.txt
[2023-03-16 23:07:35,107] [INFO] Task started: fastANI
[2023-03-16 23:07:35,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg67f0b1b8-8ab4-4654-a152-300087c08d47/OceanDNA-b2835.fa --refList OceanDNA-b2835/target_genomes_gtdb.txt --output OceanDNA-b2835/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:07:53,249] [INFO] Task succeeded: fastANI
[2023-03-16 23:07:53,261] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:07:53,261] [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
GCF_003344865.1	s__Euzebya sp003344865	96.5691	1397	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003073135.1	s__Euzebya rosea	88.7283	1301	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003074135.1	s__Euzebya tangerina	77.9376	456	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695145.1	s__JACDBB01 sp013695145	76.6926	226	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACDBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696915.1	s__JACCXR01 sp013696915	76.4556	250	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__JACCXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003553795.1	s__T1Sed10-49 sp003553795	76.4497	246	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	99.28	99.23	0.95	0.92	4	-
GCA_007126835.1	s__SLAO01 sp007126835	76.282	123	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SLAO01	95.0	98.77	98.77	0.62	0.62	2	-
GCA_009377835.1	s__WHTG01 sp009377835	76.1141	160	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__WHTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021615.1	s__QS-5-72-10 sp003021615	76.1096	116	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__QS-5-72-10	95.0	97.51	97.51	0.71	0.71	2	-
GCA_007119305.1	s__SKPY01 sp007119305	76.0621	183	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__SKPY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004300825.1	s__Egicoccus halophilus	75.9664	264	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007123425.1	s__SKLC01 sp007123425	75.9139	153	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133145.1	s__T1Sed10-49 sp007133145	75.9134	171	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__T1Sed10-49	95.0	98.98	98.60	0.85	0.78	3	-
GCF_003076135.1	s__Nocardioides gansuensis	75.5712	216	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009916105.1	s__Streptomyces sp009916105	75.4214	211	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	75.4196	310	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004605.1	s__Pseudokineococcus marinus	75.3409	186	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205275.1	s__Sphaerisporangium siamense	75.3254	288	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014650115.1	s__Streptomyces olivaceoviridis	75.3031	301	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.78	96.54	0.86	0.85	6	-
GCF_000720115.1	s__Streptomyces sp000720115	75.23	230	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308795.1	s__Nocardia thailandica	75.1992	266	1507	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:07:53,262] [INFO] GTDB search result was written to OceanDNA-b2835/result_gtdb.tsv
[2023-03-16 23:07:53,262] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:07:53,264] [INFO] DFAST_QC result json was written to OceanDNA-b2835/dqc_result.json
[2023-03-16 23:07:53,264] [INFO] DFAST_QC completed!
[2023-03-16 23:07:53,264] [INFO] Total running time: 0h2m49s