[2024-01-24 14:12:45,690] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:45,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:45,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg542b7637-d7cb-4d4c-b0bf-1bef1a10a4a2/dqc_reference
[2024-01-24 14:12:46,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:46,925] [INFO] Task started: Prodigal
[2024-01-24 14:12:46,926] [INFO] Running command: gunzip -c /var/lib/cwl/stgc09ce394-66de-425e-ae95-02f6389846e6/GCF_019968605.1_ASM1996860v1_genomic.fna.gz | prodigal -d GCF_019968605.1_ASM1996860v1_genomic.fna/cds.fna -a GCF_019968605.1_ASM1996860v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:00,437] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:00,437] [INFO] Task started: HMMsearch
[2024-01-24 14:13:00,438] [INFO] Running command: hmmsearch --tblout GCF_019968605.1_ASM1996860v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg542b7637-d7cb-4d4c-b0bf-1bef1a10a4a2/dqc_reference/reference_markers.hmm GCF_019968605.1_ASM1996860v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:00,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:00,771] [INFO] Found 6/6 markers.
[2024-01-24 14:13:00,813] [INFO] Query marker FASTA was written to GCF_019968605.1_ASM1996860v1_genomic.fna/markers.fasta
[2024-01-24 14:13:00,813] [INFO] Task started: Blastn
[2024-01-24 14:13:00,813] [INFO] Running command: blastn -query GCF_019968605.1_ASM1996860v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg542b7637-d7cb-4d4c-b0bf-1bef1a10a4a2/dqc_reference/reference_markers.fasta -out GCF_019968605.1_ASM1996860v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:01,498] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:01,502] [INFO] Selected 17 target genomes.
[2024-01-24 14:13:01,502] [INFO] Target genome list was writen to GCF_019968605.1_ASM1996860v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:01,512] [INFO] Task started: fastANI
[2024-01-24 14:13:01,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgc09ce394-66de-425e-ae95-02f6389846e6/GCF_019968605.1_ASM1996860v1_genomic.fna.gz --refList GCF_019968605.1_ASM1996860v1_genomic.fna/target_genomes.txt --output GCF_019968605.1_ASM1996860v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:15,567] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:15,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg542b7637-d7cb-4d4c-b0bf-1bef1a10a4a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:15,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg542b7637-d7cb-4d4c-b0bf-1bef1a10a4a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:15,581] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:15,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:15,582] [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 litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	100.0	1446	1446	95	conclusive
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	81.1263	736	1446	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	81.0304	726	1446	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.2013	611	1446	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	80.1252	662	1446	95	below_threshold
Polaribacter glomeratus	strain=ATCC 43844	GCA_002954665.1	102	102	type	True	80.1161	680	1446	95	below_threshold
Polaribacter glomeratus	strain=ACAM 171	GCA_007997115.1	102	102	type	True	80.1088	680	1446	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	80.0763	663	1446	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	80.0506	568	1446	95	below_threshold
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	80.0415	657	1446	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	79.8409	579	1446	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	79.6361	598	1446	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	79.5162	583	1446	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	79.5125	601	1446	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	79.4766	593	1446	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.4482	555	1446	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.3999	568	1446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:15,583] [INFO] DFAST Taxonomy check result was written to GCF_019968605.1_ASM1996860v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:15,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:15,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:15,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg542b7637-d7cb-4d4c-b0bf-1bef1a10a4a2/dqc_reference/checkm_data
[2024-01-24 14:13:15,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:15,630] [INFO] Task started: CheckM
[2024-01-24 14:13:15,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019968605.1_ASM1996860v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019968605.1_ASM1996860v1_genomic.fna/checkm_input GCF_019968605.1_ASM1996860v1_genomic.fna/checkm_result
[2024-01-24 14:13:57,872] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:57,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:57,895] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:57,895] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:57,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019968605.1_ASM1996860v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:57,896] [INFO] Task started: Blastn
[2024-01-24 14:13:57,896] [INFO] Running command: blastn -query GCF_019968605.1_ASM1996860v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg542b7637-d7cb-4d4c-b0bf-1bef1a10a4a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_019968605.1_ASM1996860v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:58,833] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:58,836] [INFO] Selected 18 target genomes.
[2024-01-24 14:13:58,836] [INFO] Target genome list was writen to GCF_019968605.1_ASM1996860v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:58,853] [INFO] Task started: fastANI
[2024-01-24 14:13:58,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgc09ce394-66de-425e-ae95-02f6389846e6/GCF_019968605.1_ASM1996860v1_genomic.fna.gz --refList GCF_019968605.1_ASM1996860v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019968605.1_ASM1996860v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:14,583] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:14,601] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:14:14,601] [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_007997085.1	s__Polaribacter sp007997085	82.1097	822	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.89	99.89	0.97	0.97	2	-
GCF_001761365.1	s__Polaribacter vadi	81.1659	731	1446	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	80.8042	763	1446	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	80.3545	702	1446	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	80.2213	610	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954665.1	s__Polaribacter glomeratus	80.1171	680	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000766795.1	s__Polaribacter sp000766795	80.0443	632	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943715.1	s__Polaribacter filamentus	80.0249	659	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981625.1	s__Polaribacter sp000981625	79.8554	494	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	79.8425	585	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106075.1	s__Polaribacter sp900106075	79.7543	606	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.66	98.45	0.96	0.92	5	-
GCF_002954605.1	s__Polaribacter butkevichii	79.7081	586	1446	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	79.6523	595	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002163675.1	s__Polaribacter sp002163675	79.6245	628	1446	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	79.5935	570	1446	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	79.4764	593	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498485.1	s__Polaribacter sp017498485	79.4263	553	1446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569185.1	s__Polaribacter sp017569185	79.3989	568	1446	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 14:14:14,606] [INFO] GTDB search result was written to GCF_019968605.1_ASM1996860v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:14,606] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:14,610] [INFO] DFAST_QC result json was written to GCF_019968605.1_ASM1996860v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:14,610] [INFO] DFAST_QC completed!
[2024-01-24 14:14:14,610] [INFO] Total running time: 0h1m29s