[2024-01-24 13:57:42,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgedd87e14-7e6b-4e97-a453-cd3f456c171f/dqc_reference
[2024-01-24 13:57:43,820] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,821] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,822] [INFO] Running command: gunzip -c /var/lib/cwl/stgb728c21c-32d1-42a4-aacf-55dc5a66095d/GCF_020532765.1_ASM2053276v1_genomic.fna.gz | prodigal -d GCF_020532765.1_ASM2053276v1_genomic.fna/cds.fna -a GCF_020532765.1_ASM2053276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:55,363] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:55,363] [INFO] Task started: HMMsearch
[2024-01-24 13:57:55,363] [INFO] Running command: hmmsearch --tblout GCF_020532765.1_ASM2053276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedd87e14-7e6b-4e97-a453-cd3f456c171f/dqc_reference/reference_markers.hmm GCF_020532765.1_ASM2053276v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:55,678] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:55,680] [INFO] Found 6/6 markers.
[2024-01-24 13:57:55,708] [INFO] Query marker FASTA was written to GCF_020532765.1_ASM2053276v1_genomic.fna/markers.fasta
[2024-01-24 13:57:55,709] [INFO] Task started: Blastn
[2024-01-24 13:57:55,709] [INFO] Running command: blastn -query GCF_020532765.1_ASM2053276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedd87e14-7e6b-4e97-a453-cd3f456c171f/dqc_reference/reference_markers.fasta -out GCF_020532765.1_ASM2053276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:56,383] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:56,388] [INFO] Selected 19 target genomes.
[2024-01-24 13:57:56,389] [INFO] Target genome list was writen to GCF_020532765.1_ASM2053276v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:56,399] [INFO] Task started: fastANI
[2024-01-24 13:57:56,399] [INFO] Running command: fastANI --query /var/lib/cwl/stgb728c21c-32d1-42a4-aacf-55dc5a66095d/GCF_020532765.1_ASM2053276v1_genomic.fna.gz --refList GCF_020532765.1_ASM2053276v1_genomic.fna/target_genomes.txt --output GCF_020532765.1_ASM2053276v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:08,687] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:08,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedd87e14-7e6b-4e97-a453-cd3f456c171f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:08,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedd87e14-7e6b-4e97-a453-cd3f456c171f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:08,708] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:08,709] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:08,709] [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 gangjinensis	strain=JCM 16152	GCA_020532765.1	574710	574710	type	True	100.0	956	959	95	conclusive
Polaribacter gangjinensis	strain=KCTC 22729	GCA_002954645.1	574710	574710	type	True	99.9912	959	959	95	conclusive
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	78.9295	496	959	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	78.9287	502	959	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	78.7041	413	959	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	78.6969	440	959	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	78.6917	450	959	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	78.6843	438	959	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	78.5703	427	959	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	78.555	403	959	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	78.5129	461	959	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	78.5116	428	959	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	78.5081	448	959	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	78.48	440	959	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	78.4757	446	959	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	78.3774	450	959	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	78.3702	433	959	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	78.3162	425	959	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	78.0369	437	959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:08,711] [INFO] DFAST Taxonomy check result was written to GCF_020532765.1_ASM2053276v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:08,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:08,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:08,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedd87e14-7e6b-4e97-a453-cd3f456c171f/dqc_reference/checkm_data
[2024-01-24 13:58:08,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:08,743] [INFO] Task started: CheckM
[2024-01-24 13:58:08,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020532765.1_ASM2053276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020532765.1_ASM2053276v1_genomic.fna/checkm_input GCF_020532765.1_ASM2053276v1_genomic.fna/checkm_result
[2024-01-24 13:58:47,366] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:47,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:47,389] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:47,389] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:47,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020532765.1_ASM2053276v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:47,390] [INFO] Task started: Blastn
[2024-01-24 13:58:47,390] [INFO] Running command: blastn -query GCF_020532765.1_ASM2053276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedd87e14-7e6b-4e97-a453-cd3f456c171f/dqc_reference/reference_markers_gtdb.fasta -out GCF_020532765.1_ASM2053276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:48,343] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:48,346] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:48,346] [INFO] Target genome list was writen to GCF_020532765.1_ASM2053276v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:48,367] [INFO] Task started: fastANI
[2024-01-24 13:58:48,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgb728c21c-32d1-42a4-aacf-55dc5a66095d/GCF_020532765.1_ASM2053276v1_genomic.fna.gz --refList GCF_020532765.1_ASM2053276v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020532765.1_ASM2053276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:57,645] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:57,664] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:57,665] [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_002954645.1	s__Polaribacter gangjinensis	99.9912	959	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015767435.1	s__Polaribacter sp015767435	85.0726	740	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873065.1	s__Polaribacter sp001873065	83.053	643	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.94	99.89	0.95	0.94	8	-
GCA_002340765.1	s__Polaribacter sp002340765	82.344	496	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.32	98.94	0.76	0.72	3	-
GCF_001761365.1	s__Polaribacter vadi	78.9554	499	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000687935.1	s__Polaribacter sp000687935	78.8588	502	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	78.7248	411	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885675.1	s__Polaribacter aestuariivivens	78.6932	437	959	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	78.6823	451	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105145.1	s__Polaribacter sp900105145	78.5546	462	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954685.1	s__Polaribacter porphyrae	78.48	440	959	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	78.4283	452	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003335085.1	s__Polaribacter sp003335085	78.082	328	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016858305.2	s__Polaribacter sp016858305	77.9218	354	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:57,667] [INFO] GTDB search result was written to GCF_020532765.1_ASM2053276v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:57,668] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:57,673] [INFO] DFAST_QC result json was written to GCF_020532765.1_ASM2053276v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:57,674] [INFO] DFAST_QC completed!
[2024-01-24 13:58:57,674] [INFO] Total running time: 0h1m15s