[2023-03-16 23:35:14,520] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:14,520] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:14,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg40fd3168-1a87-459d-84a5-6eb58b32f375/dqc_reference
[2023-03-16 23:35:15,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:15,615] [INFO] Task started: Prodigal
[2023-03-16 23:35:15,615] [INFO] Running command: cat /var/lib/cwl/stg99cc90eb-9f4c-47bc-a4df-70d7d521d432/OceanDNA-b9928.fa | prodigal -d OceanDNA-b9928/cds.fna -a OceanDNA-b9928/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:25,165] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:25,165] [INFO] Task started: HMMsearch
[2023-03-16 23:35:25,166] [INFO] Running command: hmmsearch --tblout OceanDNA-b9928/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40fd3168-1a87-459d-84a5-6eb58b32f375/dqc_reference/reference_markers.hmm OceanDNA-b9928/protein.faa > /dev/null
[2023-03-16 23:35:25,316] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:25,317] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg99cc90eb-9f4c-47bc-a4df-70d7d521d432/OceanDNA-b9928.fa]
[2023-03-16 23:35:25,331] [INFO] Query marker FASTA was written to OceanDNA-b9928/markers.fasta
[2023-03-16 23:35:25,331] [INFO] Task started: Blastn
[2023-03-16 23:35:25,331] [INFO] Running command: blastn -query OceanDNA-b9928/markers.fasta -db /var/lib/cwl/stg40fd3168-1a87-459d-84a5-6eb58b32f375/dqc_reference/reference_markers.fasta -out OceanDNA-b9928/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:25,850] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:25,851] [INFO] Selected 14 target genomes.
[2023-03-16 23:35:25,851] [INFO] Target genome list was writen to OceanDNA-b9928/target_genomes.txt
[2023-03-16 23:35:25,859] [INFO] Task started: fastANI
[2023-03-16 23:35:25,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg99cc90eb-9f4c-47bc-a4df-70d7d521d432/OceanDNA-b9928.fa --refList OceanDNA-b9928/target_genomes.txt --output OceanDNA-b9928/fastani_result.tsv --threads 1
[2023-03-16 23:35:33,997] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:33,997] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40fd3168-1a87-459d-84a5-6eb58b32f375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:33,997] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40fd3168-1a87-459d-84a5-6eb58b32f375/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:34,006] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:34,006] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:35:34,006] [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
Polaribacter irgensii	strain=23-P	GCA_000153225.1	531	531	type	True	79.5687	265	425	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	79.4402	277	425	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	79.3157	288	425	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	79.295	287	425	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	79.1933	264	425	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	79.163	258	425	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	79.0746	257	425	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	79.0222	260	425	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	78.991	263	425	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.9321	259	425	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.8135	250	425	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.7585	265	425	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.7504	252	425	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.7472	264	425	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:35:34,006] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9928/tc_result.tsv
[2023-03-16 23:35:34,006] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:34,006] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:34,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40fd3168-1a87-459d-84a5-6eb58b32f375/dqc_reference/checkm_data
[2023-03-16 23:35:34,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:34,011] [INFO] Task started: CheckM
[2023-03-16 23:35:34,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9928/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9928/checkm_input OceanDNA-b9928/checkm_result
[2023-03-16 23:36:02,304] [INFO] Task succeeded: CheckM
[2023-03-16 23:36:02,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.57%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 23:36:02,306] [INFO] ===== Completeness check finished =====
[2023-03-16 23:36:02,306] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:36:02,307] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9928/markers.fasta)
[2023-03-16 23:36:02,308] [INFO] Task started: Blastn
[2023-03-16 23:36:02,308] [INFO] Running command: blastn -query OceanDNA-b9928/markers.fasta -db /var/lib/cwl/stg40fd3168-1a87-459d-84a5-6eb58b32f375/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9928/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:36:03,022] [INFO] Task succeeded: Blastn
[2023-03-16 23:36:03,023] [INFO] Selected 12 target genomes.
[2023-03-16 23:36:03,023] [INFO] Target genome list was writen to OceanDNA-b9928/target_genomes_gtdb.txt
[2023-03-16 23:36:03,079] [INFO] Task started: fastANI
[2023-03-16 23:36:03,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg99cc90eb-9f4c-47bc-a4df-70d7d521d432/OceanDNA-b9928.fa --refList OceanDNA-b9928/target_genomes_gtdb.txt --output OceanDNA-b9928/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:36:10,273] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:10,281] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:36:10,281] [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_002831685.1	s__Polaribacter sp002831685	81.4398	334	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997075.1	s__Polaribacter sp007997075	81.4115	333	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181765.1	s__Polaribacter sp905181765	81.2826	254	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.49	96.49	0.69	0.69	2	-
GCF_002163835.1	s__Polaribacter sp002163835	79.7773	283	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352875.1	s__Polaribacter sp014352875	79.4402	277	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	79.3157	288	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000766795.1	s__Polaribacter sp000766795	79.2786	270	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	79.2689	267	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	79.2253	264	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002814075.1	s__Polaribacter sejongensis	79.21	263	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_002005425.1	s__Polaribacter sp002005425	79.1857	280	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	96.81	96.81	0.92	0.92	2	-
GCF_016858305.2	s__Polaribacter sp016858305	79.0979	262	425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:36:10,281] [INFO] GTDB search result was written to OceanDNA-b9928/result_gtdb.tsv
[2023-03-16 23:36:10,281] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:36:10,283] [INFO] DFAST_QC result json was written to OceanDNA-b9928/dqc_result.json
[2023-03-16 23:36:10,283] [INFO] DFAST_QC completed!
[2023-03-16 23:36:10,283] [INFO] Total running time: 0h0m56s