[2024-01-24 15:26:54,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:54,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:54,828] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf7a88d5-db3e-4257-8734-3d80ed55bcfb/dqc_reference
[2024-01-24 15:26:56,251] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,252] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,252] [INFO] Running command: gunzip -c /var/lib/cwl/stg28729255-eb64-4ba4-9244-032179859a62/GCF_007993035.1_ASM799303v1_genomic.fna.gz | prodigal -d GCF_007993035.1_ASM799303v1_genomic.fna/cds.fna -a GCF_007993035.1_ASM799303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:05,132] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:05,133] [INFO] Task started: HMMsearch
[2024-01-24 15:27:05,133] [INFO] Running command: hmmsearch --tblout GCF_007993035.1_ASM799303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf7a88d5-db3e-4257-8734-3d80ed55bcfb/dqc_reference/reference_markers.hmm GCF_007993035.1_ASM799303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:05,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:05,390] [INFO] Found 6/6 markers.
[2024-01-24 15:27:05,417] [INFO] Query marker FASTA was written to GCF_007993035.1_ASM799303v1_genomic.fna/markers.fasta
[2024-01-24 15:27:05,417] [INFO] Task started: Blastn
[2024-01-24 15:27:05,418] [INFO] Running command: blastn -query GCF_007993035.1_ASM799303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf7a88d5-db3e-4257-8734-3d80ed55bcfb/dqc_reference/reference_markers.fasta -out GCF_007993035.1_ASM799303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:06,066] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:06,070] [INFO] Selected 27 target genomes.
[2024-01-24 15:27:06,070] [INFO] Target genome list was writen to GCF_007993035.1_ASM799303v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:06,449] [INFO] Task started: fastANI
[2024-01-24 15:27:06,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg28729255-eb64-4ba4-9244-032179859a62/GCF_007993035.1_ASM799303v1_genomic.fna.gz --refList GCF_007993035.1_ASM799303v1_genomic.fna/target_genomes.txt --output GCF_007993035.1_ASM799303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:22,097] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:22,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf7a88d5-db3e-4257-8734-3d80ed55bcfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:22,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf7a88d5-db3e-4257-8734-3d80ed55bcfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:22,115] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:22,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:22,115] [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
Vicingus serpentipes	strain=NCIMB 15042	GCA_007993035.1	1926625	1926625	type	True	100.0	961	962	95	conclusive
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.4567	58	962	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.4133	69	962	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.4122	64	962	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.3133	84	962	95	below_threshold
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	76.2669	62	962	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.1202	85	962	95	below_threshold
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	76.1106	70	962	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.04	54	962	95	below_threshold
Putridiphycobacter roseus	strain=SM1701	GCA_003234935.1	2219161	2219161	type	True	76.0344	50	962	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.0052	60	962	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	75.9971	70	962	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.8496	88	962	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	75.8462	79	962	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	75.8354	78	962	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	75.8057	95	962	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	75.7549	56	962	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	75.7088	81	962	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	75.6753	90	962	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	75.6508	58	962	95	below_threshold
Acidiluteibacter ferrifornacis	strain=S-15	GCA_009909615.1	2692424	2692424	type	True	75.6477	50	962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:22,119] [INFO] DFAST Taxonomy check result was written to GCF_007993035.1_ASM799303v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:22,119] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:22,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:22,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf7a88d5-db3e-4257-8734-3d80ed55bcfb/dqc_reference/checkm_data
[2024-01-24 15:27:22,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:22,163] [INFO] Task started: CheckM
[2024-01-24 15:27:22,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007993035.1_ASM799303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007993035.1_ASM799303v1_genomic.fna/checkm_input GCF_007993035.1_ASM799303v1_genomic.fna/checkm_result
[2024-01-24 15:27:52,164] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:52,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:52,184] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:52,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:52,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007993035.1_ASM799303v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:52,186] [INFO] Task started: Blastn
[2024-01-24 15:27:52,186] [INFO] Running command: blastn -query GCF_007993035.1_ASM799303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf7a88d5-db3e-4257-8734-3d80ed55bcfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007993035.1_ASM799303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:53,029] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:53,033] [INFO] Selected 19 target genomes.
[2024-01-24 15:27:53,033] [INFO] Target genome list was writen to GCF_007993035.1_ASM799303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:53,052] [INFO] Task started: fastANI
[2024-01-24 15:27:53,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg28729255-eb64-4ba4-9244-032179859a62/GCF_007993035.1_ASM799303v1_genomic.fna.gz --refList GCF_007993035.1_ASM799303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007993035.1_ASM799303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:02,412] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:02,424] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:02,424] [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_007993035.1	s__Vicingus serpentipes	100.0	961	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479915.1	s__GCA-002793235 sp905479915	77.3705	216	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479995.1	s__GCA-002793235 sp905479995	77.2692	225	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002402165.1	s__GCA-002793235 sp002402165	77.2281	202	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359215.1	s__BRH-c54 sp002359215	77.1115	186	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	99.41	98.22	0.97	0.91	4	-
GCA_015075325.1	s__Vicingus sp015075325	76.9752	255	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	96.71	96.71	0.84	0.84	2	-
GCA_000961845.1	s__BRH-c54 sp000961845	76.9239	173	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401955.1	s__GCA-002793235 sp002401955	76.8484	226	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002770955.1	s__BRH-c54 sp002770955	76.817	162	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	99.41	99.41	0.88	0.88	2	-
GCA_016763135.1	s__GCA-002793235 sp016763135	76.7883	167	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183805.1	s__Vicingus sp016183805	76.6889	222	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763795.1	s__GCA-002793235 sp016763795	76.6294	178	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	76.2472	68	962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:02,426] [INFO] GTDB search result was written to GCF_007993035.1_ASM799303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:02,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:02,440] [INFO] DFAST_QC result json was written to GCF_007993035.1_ASM799303v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:02,440] [INFO] DFAST_QC completed!
[2024-01-24 15:28:02,441] [INFO] Total running time: 0h1m8s