[2024-01-24 11:43:50,653] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:50,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:50,656] [INFO] DQC Reference Directory: /var/lib/cwl/stgedb7895b-4d83-4b98-b945-67e36f833f01/dqc_reference
[2024-01-24 11:43:51,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:51,905] [INFO] Task started: Prodigal
[2024-01-24 11:43:51,905] [INFO] Running command: gunzip -c /var/lib/cwl/stge81cfeff-7169-4c2f-a2ba-ea96091eea0f/GCF_024362345.1_ASM2436234v1_genomic.fna.gz | prodigal -d GCF_024362345.1_ASM2436234v1_genomic.fna/cds.fna -a GCF_024362345.1_ASM2436234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:00,610] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:00,610] [INFO] Task started: HMMsearch
[2024-01-24 11:44:00,610] [INFO] Running command: hmmsearch --tblout GCF_024362345.1_ASM2436234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedb7895b-4d83-4b98-b945-67e36f833f01/dqc_reference/reference_markers.hmm GCF_024362345.1_ASM2436234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:00,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:00,811] [INFO] Found 6/6 markers.
[2024-01-24 11:44:00,836] [INFO] Query marker FASTA was written to GCF_024362345.1_ASM2436234v1_genomic.fna/markers.fasta
[2024-01-24 11:44:00,837] [INFO] Task started: Blastn
[2024-01-24 11:44:00,837] [INFO] Running command: blastn -query GCF_024362345.1_ASM2436234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedb7895b-4d83-4b98-b945-67e36f833f01/dqc_reference/reference_markers.fasta -out GCF_024362345.1_ASM2436234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:01,467] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:01,470] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:01,470] [INFO] Target genome list was writen to GCF_024362345.1_ASM2436234v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:01,503] [INFO] Task started: fastANI
[2024-01-24 11:44:01,503] [INFO] Running command: fastANI --query /var/lib/cwl/stge81cfeff-7169-4c2f-a2ba-ea96091eea0f/GCF_024362345.1_ASM2436234v1_genomic.fna.gz --refList GCF_024362345.1_ASM2436234v1_genomic.fna/target_genomes.txt --output GCF_024362345.1_ASM2436234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:11,730] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:11,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedb7895b-4d83-4b98-b945-67e36f833f01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:11,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedb7895b-4d83-4b98-b945-67e36f833f01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:11,742] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:44:11,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:11,742] [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 dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	100.0	1022	1029	95	conclusive
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	100.0	1027	1029	95	conclusive
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	99.9999	1027	1029	95	conclusive
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	81.8746	655	1029	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	81.7909	670	1029	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	81.2036	687	1029	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	81.1427	679	1029	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	80.4118	636	1029	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	80.3877	634	1029	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	80.2683	616	1029	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	80.0857	584	1029	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	79.9335	548	1029	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	79.6229	535	1029	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	79.2852	534	1029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:11,744] [INFO] DFAST Taxonomy check result was written to GCF_024362345.1_ASM2436234v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:11,744] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:11,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:11,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedb7895b-4d83-4b98-b945-67e36f833f01/dqc_reference/checkm_data
[2024-01-24 11:44:11,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:11,778] [INFO] Task started: CheckM
[2024-01-24 11:44:11,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024362345.1_ASM2436234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024362345.1_ASM2436234v1_genomic.fna/checkm_input GCF_024362345.1_ASM2436234v1_genomic.fna/checkm_result
[2024-01-24 11:44:40,027] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:40,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:40,045] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:40,045] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:40,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024362345.1_ASM2436234v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:40,046] [INFO] Task started: Blastn
[2024-01-24 11:44:40,046] [INFO] Running command: blastn -query GCF_024362345.1_ASM2436234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedb7895b-4d83-4b98-b945-67e36f833f01/dqc_reference/reference_markers_gtdb.fasta -out GCF_024362345.1_ASM2436234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:40,915] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:40,918] [INFO] Selected 11 target genomes.
[2024-01-24 11:44:40,918] [INFO] Target genome list was writen to GCF_024362345.1_ASM2436234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:40,926] [INFO] Task started: fastANI
[2024-01-24 11:44:40,926] [INFO] Running command: fastANI --query /var/lib/cwl/stge81cfeff-7169-4c2f-a2ba-ea96091eea0f/GCF_024362345.1_ASM2436234v1_genomic.fna.gz --refList GCF_024362345.1_ASM2436234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024362345.1_ASM2436234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:49,059] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:49,069] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:49,069] [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_001280865.1	s__Polaribacter dokdonensis	99.9999	1026	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000152945.2	s__Polaribacter sp000152945	86.7325	895	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	81.8819	672	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018861005.1	s__Polaribacter vadi_A	81.7313	673	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761365.1	s__Polaribacter vadi	81.2097	687	1029	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	80.8773	692	1029	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	80.4163	617	1029	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	80.4023	637	1029	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	80.0979	582	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	79.9479	546	1029	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	79.896	542	1029	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 11:44:49,070] [INFO] GTDB search result was written to GCF_024362345.1_ASM2436234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:49,071] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:49,074] [INFO] DFAST_QC result json was written to GCF_024362345.1_ASM2436234v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:49,074] [INFO] DFAST_QC completed!
[2024-01-24 11:44:49,074] [INFO] Total running time: 0h0m58s