[2023-03-16 13:29:11,831] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:29:11,831] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:29:11,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d7485f9-7a3b-4b7d-abfa-fe3b45b5a7c2/dqc_reference
[2023-03-16 13:29:13,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:29:13,486] [INFO] Task started: Prodigal
[2023-03-16 13:29:13,486] [INFO] Running command: cat /var/lib/cwl/stg9f204b55-5c8a-4271-946a-28f62c11ef30/OceanDNA-b2517.fa | prodigal -d OceanDNA-b2517/cds.fna -a OceanDNA-b2517/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:29:22,775] [INFO] Task succeeded: Prodigal
[2023-03-16 13:29:22,775] [INFO] Task started: HMMsearch
[2023-03-16 13:29:22,775] [INFO] Running command: hmmsearch --tblout OceanDNA-b2517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d7485f9-7a3b-4b7d-abfa-fe3b45b5a7c2/dqc_reference/reference_markers.hmm OceanDNA-b2517/protein.faa > /dev/null
[2023-03-16 13:29:22,940] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:29:22,940] [INFO] Found 6/6 markers.
[2023-03-16 13:29:22,956] [INFO] Query marker FASTA was written to OceanDNA-b2517/markers.fasta
[2023-03-16 13:29:22,956] [INFO] Task started: Blastn
[2023-03-16 13:29:22,956] [INFO] Running command: blastn -query OceanDNA-b2517/markers.fasta -db /var/lib/cwl/stg5d7485f9-7a3b-4b7d-abfa-fe3b45b5a7c2/dqc_reference/reference_markers.fasta -out OceanDNA-b2517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:29:23,782] [INFO] Task succeeded: Blastn
[2023-03-16 13:29:23,783] [INFO] Selected 27 target genomes.
[2023-03-16 13:29:23,783] [INFO] Target genome list was writen to OceanDNA-b2517/target_genomes.txt
[2023-03-16 13:29:23,797] [INFO] Task started: fastANI
[2023-03-16 13:29:23,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f204b55-5c8a-4271-946a-28f62c11ef30/OceanDNA-b2517.fa --refList OceanDNA-b2517/target_genomes.txt --output OceanDNA-b2517/fastani_result.tsv --threads 1
[2023-03-16 13:29:40,491] [INFO] Task succeeded: fastANI
[2023-03-16 13:29:40,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d7485f9-7a3b-4b7d-abfa-fe3b45b5a7c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:29:40,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d7485f9-7a3b-4b7d-abfa-fe3b45b5a7c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:29:40,502] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:29:40,502] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 13:29:40,502] [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
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.7262	98	336	95	below_threshold
Ornithinimicrobium flavum	strain=CPCC 203535	GCA_004526345.1	1288636	1288636	type	True	77.3968	70	336	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	77.3355	68	336	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	77.2	71	336	95	below_threshold
Ornithinimicrobium cerasi	strain=CPCC 203383	GCA_003702705.1	2248773	2248773	type	True	77.1565	67	336	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	77.047	103	336	95	below_threshold
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	77.0195	75	336	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	77.0176	96	336	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	76.971	99	336	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	76.9642	73	336	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	76.9344	74	336	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.9153	77	336	95	below_threshold
Ornithinicoccus halotolerans	strain=EGI 80423	GCA_009602535.1	1748220	1748220	type	True	76.8738	70	336	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	76.8374	51	336	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	76.6771	62	336	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	76.6081	90	336	95	below_threshold
Serinicoccus profundi	strain=CGMCC 4.5582	GCA_008001015.1	1078471	1078471	type	True	76.6073	92	336	95	below_threshold
Ornithinimicrobium pratense	strain=W204	GCA_008843165.1	2593973	2593973	type	True	76.5696	63	336	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	76.1903	52	336	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 13:29:40,502] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2517/tc_result.tsv
[2023-03-16 13:29:40,502] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:29:40,503] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:29:40,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d7485f9-7a3b-4b7d-abfa-fe3b45b5a7c2/dqc_reference/checkm_data
[2023-03-16 13:29:40,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:29:40,508] [INFO] Task started: CheckM
[2023-03-16 13:29:40,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2517/checkm_input OceanDNA-b2517/checkm_result
[2023-03-16 13:30:12,266] [INFO] Task succeeded: CheckM
[2023-03-16 13:30:12,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 5.53%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 13:30:12,268] [INFO] ===== Completeness check finished =====
[2023-03-16 13:30:12,269] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:30:12,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2517/markers.fasta)
[2023-03-16 13:30:12,269] [INFO] Task started: Blastn
[2023-03-16 13:30:12,269] [INFO] Running command: blastn -query OceanDNA-b2517/markers.fasta -db /var/lib/cwl/stg5d7485f9-7a3b-4b7d-abfa-fe3b45b5a7c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:30:13,596] [INFO] Task succeeded: Blastn
[2023-03-16 13:30:13,597] [INFO] Selected 26 target genomes.
[2023-03-16 13:30:13,597] [INFO] Target genome list was writen to OceanDNA-b2517/target_genomes_gtdb.txt
[2023-03-16 13:30:13,832] [INFO] Task started: fastANI
[2023-03-16 13:30:13,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f204b55-5c8a-4271-946a-28f62c11ef30/OceanDNA-b2517.fa --refList OceanDNA-b2517/target_genomes_gtdb.txt --output OceanDNA-b2517/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:30:39,417] [INFO] Task succeeded: fastANI
[2023-03-16 13:30:39,429] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:30:39,429] [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_004526345.1	s__Serinicoccus flavus	77.3968	70	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	77.3355	68	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636495.1	s__Ornithinimicrobium tianjinense	77.2	71	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003702705.1	s__Ornithinimicrobium cerasi	77.1565	67	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	96.64	96.64	0.85	0.85	2	-
GCF_006716185.1	s__Ornithinicoccus hortensis	77.047	103	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007197575.1	s__Ornithinicoccus sp007197575	77.0195	75	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942405.1	s__Ornithinimicrobium sp001942405	76.959	73	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	97.63	97.63	0.88	0.88	2	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	76.9344	74	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201035.1	s__Phycicoccus sp013201035	76.8752	54	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009602535.1	s__Ornithinicoccus_A halotolerans	76.8738	70	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352835.1	s__Ornithinicoccus muralis	76.8374	51	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004322775.1	s__Serinicoccus sp004322775	76.7967	71	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001483745.1	s__Serinicoccus chungangensis_A	76.7596	87	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	76.6771	62	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_008919445.1	s__Serinicoccus sp008919445	76.6081	90	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008001015.1	s__Serinicoccus profundi	76.6073	92	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.17	98.35	0.97	0.94	3	-
GCF_008843165.1	s__Serinicoccus pratense	76.5696	63	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429605.1	s__Pedococcus sp001429605	76.4008	71	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.23	98.23	0.91	0.91	2	-
GCF_000768705.1	s__Knoellia sinensis	76.1903	52	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408565.1	s__Janibacter alkaliphilus	76.1499	58	336	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 13:30:39,429] [INFO] GTDB search result was written to OceanDNA-b2517/result_gtdb.tsv
[2023-03-16 13:30:39,430] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:30:39,432] [INFO] DFAST_QC result json was written to OceanDNA-b2517/dqc_result.json
[2023-03-16 13:30:39,432] [INFO] DFAST_QC completed!
[2023-03-16 13:30:39,432] [INFO] Total running time: 0h1m28s