[2024-01-24 11:44:38,160] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb4e2541-bbeb-4347-9221-244d1011e3db/dqc_reference
[2024-01-24 11:44:41,486] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,487] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgf30b4f14-0de7-4a1d-9299-ded23c504df3/GCF_004366575.1_ASM436657v1_genomic.fna.gz | prodigal -d GCF_004366575.1_ASM436657v1_genomic.fna/cds.fna -a GCF_004366575.1_ASM436657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:45:03,731] [INFO] Task succeeded: Prodigal
[2024-01-24 11:45:03,732] [INFO] Task started: HMMsearch
[2024-01-24 11:45:03,732] [INFO] Running command: hmmsearch --tblout GCF_004366575.1_ASM436657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb4e2541-bbeb-4347-9221-244d1011e3db/dqc_reference/reference_markers.hmm GCF_004366575.1_ASM436657v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:45:04,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:45:04,038] [INFO] Found 6/6 markers.
[2024-01-24 11:45:04,086] [INFO] Query marker FASTA was written to GCF_004366575.1_ASM436657v1_genomic.fna/markers.fasta
[2024-01-24 11:45:04,086] [INFO] Task started: Blastn
[2024-01-24 11:45:04,086] [INFO] Running command: blastn -query GCF_004366575.1_ASM436657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb4e2541-bbeb-4347-9221-244d1011e3db/dqc_reference/reference_markers.fasta -out GCF_004366575.1_ASM436657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:04,703] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:04,707] [INFO] Selected 15 target genomes.
[2024-01-24 11:45:04,707] [INFO] Target genome list was writen to GCF_004366575.1_ASM436657v1_genomic.fna/target_genomes.txt
[2024-01-24 11:45:04,714] [INFO] Task started: fastANI
[2024-01-24 11:45:04,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30b4f14-0de7-4a1d-9299-ded23c504df3/GCF_004366575.1_ASM436657v1_genomic.fna.gz --refList GCF_004366575.1_ASM436657v1_genomic.fna/target_genomes.txt --output GCF_004366575.1_ASM436657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:17,196] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:17,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb4e2541-bbeb-4347-9221-244d1011e3db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:17,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb4e2541-bbeb-4347-9221-244d1011e3db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:17,218] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:45:17,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:17,218] [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
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	100.0	1592	1594	95	conclusive
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	99.9976	1591	1594	95	conclusive
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	80.4234	715	1594	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	78.6645	405	1594	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	78.5957	425	1594	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	77.9131	357	1594	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	77.5858	360	1594	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	77.4465	310	1594	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	77.2943	236	1594	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	77.1714	222	1594	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.6948	116	1594	95	below_threshold
Marinoscillum pacificum	strain=MRN461	GCA_024714495.1	392723	392723	type	True	75.6572	56	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,222] [INFO] DFAST Taxonomy check result was written to GCF_004366575.1_ASM436657v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:17,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:17,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:17,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb4e2541-bbeb-4347-9221-244d1011e3db/dqc_reference/checkm_data
[2024-01-24 11:45:17,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:17,276] [INFO] Task started: CheckM
[2024-01-24 11:45:17,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366575.1_ASM436657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366575.1_ASM436657v1_genomic.fna/checkm_input GCF_004366575.1_ASM436657v1_genomic.fna/checkm_result
[2024-01-24 11:46:22,439] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:22,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:22,459] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:22,460] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:22,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366575.1_ASM436657v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:22,461] [INFO] Task started: Blastn
[2024-01-24 11:46:22,461] [INFO] Running command: blastn -query GCF_004366575.1_ASM436657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb4e2541-bbeb-4347-9221-244d1011e3db/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366575.1_ASM436657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:23,244] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:23,250] [INFO] Selected 16 target genomes.
[2024-01-24 11:46:23,250] [INFO] Target genome list was writen to GCF_004366575.1_ASM436657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:23,261] [INFO] Task started: fastANI
[2024-01-24 11:46:23,261] [INFO] Running command: fastANI --query /var/lib/cwl/stgf30b4f14-0de7-4a1d-9299-ded23c504df3/GCF_004366575.1_ASM436657v1_genomic.fna.gz --refList GCF_004366575.1_ASM436657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004366575.1_ASM436657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:36,408] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:36,429] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:36,429] [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_900148515.1	s__Algoriphagus zhangzhouensis	99.9976	1591	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000429465.1	s__Algoriphagus vanfongensis	80.4074	719	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115305.1	s__Algoriphagus ornithinivorans	78.6858	403	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
GCF_007655305.1	s__Algoriphagus sp007655305	78.5957	425	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014206875.1	s__Algoriphagus iocasae	77.9057	357	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	77.5935	359	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571135.1	s__Algoriphagus kandeliae	77.4465	310	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	77.4453	247	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	77.3956	249	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429405.1	s__Algoriphagus marincola	77.3945	280	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
GCF_002150685.1	s__Algoriphagus antarcticus	77.2966	235	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013373065.1	s__Algoriphagus sp013373065	77.2865	264	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526355.1	s__Algoriphagus marincola_A	77.2675	274	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018336015.1	s__Algoriphagus sp018336015	77.2515	218	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373335.1	s__Algoriphagus sp013373335	77.2182	215	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150505.1	s__Algoriphagus ratkowskyi	77.1535	222	1594	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:36,431] [INFO] GTDB search result was written to GCF_004366575.1_ASM436657v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:36,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:36,436] [INFO] DFAST_QC result json was written to GCF_004366575.1_ASM436657v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:36,436] [INFO] DFAST_QC completed!
[2024-01-24 11:46:36,436] [INFO] Total running time: 0h1m58s