[2024-01-24 13:49:16,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:16,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:16,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg97e04fbf-9c20-4c81-a0d5-757c1275f8ca/dqc_reference
[2024-01-24 13:49:17,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:17,789] [INFO] Task started: Prodigal
[2024-01-24 13:49:17,789] [INFO] Running command: gunzip -c /var/lib/cwl/stge1f02f7e-4595-4658-a2d3-d8c75b082d71/GCF_000429445.1_ASM42944v1_genomic.fna.gz | prodigal -d GCF_000429445.1_ASM42944v1_genomic.fna/cds.fna -a GCF_000429445.1_ASM42944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:49,542] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:49,543] [INFO] Task started: HMMsearch
[2024-01-24 13:49:49,543] [INFO] Running command: hmmsearch --tblout GCF_000429445.1_ASM42944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97e04fbf-9c20-4c81-a0d5-757c1275f8ca/dqc_reference/reference_markers.hmm GCF_000429445.1_ASM42944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:49,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:49,875] [INFO] Found 6/6 markers.
[2024-01-24 13:49:49,925] [INFO] Query marker FASTA was written to GCF_000429445.1_ASM42944v1_genomic.fna/markers.fasta
[2024-01-24 13:49:49,925] [INFO] Task started: Blastn
[2024-01-24 13:49:49,926] [INFO] Running command: blastn -query GCF_000429445.1_ASM42944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97e04fbf-9c20-4c81-a0d5-757c1275f8ca/dqc_reference/reference_markers.fasta -out GCF_000429445.1_ASM42944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,572] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,577] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:50,577] [INFO] Target genome list was writen to GCF_000429445.1_ASM42944v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:50,585] [INFO] Task started: fastANI
[2024-01-24 13:49:50,585] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f02f7e-4595-4658-a2d3-d8c75b082d71/GCF_000429445.1_ASM42944v1_genomic.fna.gz --refList GCF_000429445.1_ASM42944v1_genomic.fna/target_genomes.txt --output GCF_000429445.1_ASM42944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:05,148] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:05,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97e04fbf-9c20-4c81-a0d5-757c1275f8ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:05,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97e04fbf-9c20-4c81-a0d5-757c1275f8ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:05,160] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:05,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:05,161] [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 terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	100.0	1896	1900	95	conclusive
Algoriphagus oliviformis	strain=H41	GCA_017254915.1	2811231	2811231	type	True	79.2888	773	1900	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	79.183	753	1900	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	78.3863	452	1900	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	78.3101	482	1900	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	78.2277	439	1900	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	78.1363	477	1900	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	77.7878	277	1900	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	77.564	232	1900	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.5393	165	1900	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.4773	164	1900	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	77.2518	191	1900	95	below_threshold
Algoriphagus marinus	strain=am2	GCA_001936475.1	1925762	1925762	type	True	77.1168	143	1900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:05,163] [INFO] DFAST Taxonomy check result was written to GCF_000429445.1_ASM42944v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:05,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:05,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:05,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97e04fbf-9c20-4c81-a0d5-757c1275f8ca/dqc_reference/checkm_data
[2024-01-24 13:50:05,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:05,227] [INFO] Task started: CheckM
[2024-01-24 13:50:05,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429445.1_ASM42944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429445.1_ASM42944v1_genomic.fna/checkm_input GCF_000429445.1_ASM42944v1_genomic.fna/checkm_result
[2024-01-24 13:51:29,825] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:29,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:29,847] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:29,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:29,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429445.1_ASM42944v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:29,848] [INFO] Task started: Blastn
[2024-01-24 13:51:29,848] [INFO] Running command: blastn -query GCF_000429445.1_ASM42944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97e04fbf-9c20-4c81-a0d5-757c1275f8ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429445.1_ASM42944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:30,604] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:30,608] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:30,609] [INFO] Target genome list was writen to GCF_000429445.1_ASM42944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:30,651] [INFO] Task started: fastANI
[2024-01-24 13:51:30,652] [INFO] Running command: fastANI --query /var/lib/cwl/stge1f02f7e-4595-4658-a2d3-d8c75b082d71/GCF_000429445.1_ASM42944v1_genomic.fna.gz --refList GCF_000429445.1_ASM42944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429445.1_ASM42944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:43,752] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:43,766] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:43,766] [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_000429445.1	s__Algoriphagus terrigena	100.0	1896	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002002735.1	s__Algoriphagus sp002002735	80.5088	816	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254915.1	s__Algoriphagus sp017254915	79.2796	775	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254835.1	s__Algoriphagus aestuariicola	79.1926	752	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108085.1	s__Algoriphagus boritolerans	78.3863	452	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCF_003583985.1	s__Algoriphagus lacus	78.3207	480	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103735.1	s__Algoriphagus alkaliphilus	78.2306	441	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCF_003259255.1	s__Algoriphagus litoralis	78.1388	476	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253485.1	s__Algoriphagus aquaeductus	78.1314	411	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	77.8605	363	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429465.1	s__Algoriphagus vanfongensis	77.579	230	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	77.464	164	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009885605.1	s__Algoriphagus sp009885605	77.4481	165	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	77.2742	191	1900	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:43,768] [INFO] GTDB search result was written to GCF_000429445.1_ASM42944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:43,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:43,772] [INFO] DFAST_QC result json was written to GCF_000429445.1_ASM42944v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:43,772] [INFO] DFAST_QC completed!
[2024-01-24 13:51:43,773] [INFO] Total running time: 0h2m27s