[2024-01-24 14:11:46,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,888] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,888] [INFO] DQC Reference Directory: /var/lib/cwl/stg04b377f3-4739-433c-a89e-1570f3f93646/dqc_reference
[2024-01-24 14:11:48,070] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:48,071] [INFO] Task started: Prodigal
[2024-01-24 14:11:48,071] [INFO] Running command: gunzip -c /var/lib/cwl/stg182ed951-94f7-43c2-b497-33ee9942e5f4/GCF_000429425.1_ASM42942v1_genomic.fna.gz | prodigal -d GCF_000429425.1_ASM42942v1_genomic.fna/cds.fna -a GCF_000429425.1_ASM42942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:08,680] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:08,680] [INFO] Task started: HMMsearch
[2024-01-24 14:12:08,680] [INFO] Running command: hmmsearch --tblout GCF_000429425.1_ASM42942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04b377f3-4739-433c-a89e-1570f3f93646/dqc_reference/reference_markers.hmm GCF_000429425.1_ASM42942v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:09,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:09,052] [INFO] Found 6/6 markers.
[2024-01-24 14:12:09,087] [INFO] Query marker FASTA was written to GCF_000429425.1_ASM42942v1_genomic.fna/markers.fasta
[2024-01-24 14:12:09,087] [INFO] Task started: Blastn
[2024-01-24 14:12:09,088] [INFO] Running command: blastn -query GCF_000429425.1_ASM42942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04b377f3-4739-433c-a89e-1570f3f93646/dqc_reference/reference_markers.fasta -out GCF_000429425.1_ASM42942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:09,682] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:09,685] [INFO] Selected 17 target genomes.
[2024-01-24 14:12:09,685] [INFO] Target genome list was writen to GCF_000429425.1_ASM42942v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:09,697] [INFO] Task started: fastANI
[2024-01-24 14:12:09,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg182ed951-94f7-43c2-b497-33ee9942e5f4/GCF_000429425.1_ASM42942v1_genomic.fna.gz --refList GCF_000429425.1_ASM42942v1_genomic.fna/target_genomes.txt --output GCF_000429425.1_ASM42942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:24,253] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:24,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04b377f3-4739-433c-a89e-1570f3f93646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:24,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04b377f3-4739-433c-a89e-1570f3f93646/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:24,268] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:24,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:24,269] [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 mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	100.0	1372	1373	95	conclusive
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	80.1896	642	1373	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	78.3668	452	1373	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	78.3201	275	1373	95	below_threshold
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	78.189	350	1373	95	below_threshold
Algoriphagus oliviformis	strain=H41	GCA_017254915.1	2811231	2811231	type	True	77.915	305	1373	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	77.8964	428	1373	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	77.6639	338	1373	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	77.6513	295	1373	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	77.6078	323	1373	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	77.5518	232	1373	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	77.5503	219	1373	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	77.5307	343	1373	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	77.5251	267	1373	95	below_threshold
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	77.1573	212	1373	95	below_threshold
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	77.0725	204	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:24,271] [INFO] DFAST Taxonomy check result was written to GCF_000429425.1_ASM42942v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:24,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:24,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:24,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04b377f3-4739-433c-a89e-1570f3f93646/dqc_reference/checkm_data
[2024-01-24 14:12:24,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:24,317] [INFO] Task started: CheckM
[2024-01-24 14:12:24,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429425.1_ASM42942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429425.1_ASM42942v1_genomic.fna/checkm_input GCF_000429425.1_ASM42942v1_genomic.fna/checkm_result
[2024-01-24 14:13:24,980] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:24,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:25,012] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:25,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:25,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429425.1_ASM42942v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:25,013] [INFO] Task started: Blastn
[2024-01-24 14:13:25,014] [INFO] Running command: blastn -query GCF_000429425.1_ASM42942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg04b377f3-4739-433c-a89e-1570f3f93646/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429425.1_ASM42942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:25,819] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:25,823] [INFO] Selected 19 target genomes.
[2024-01-24 14:13:25,823] [INFO] Target genome list was writen to GCF_000429425.1_ASM42942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:25,845] [INFO] Task started: fastANI
[2024-01-24 14:13:25,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg182ed951-94f7-43c2-b497-33ee9942e5f4/GCF_000429425.1_ASM42942v1_genomic.fna.gz --refList GCF_000429425.1_ASM42942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429425.1_ASM42942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:40,392] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:40,413] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:40,413] [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_000429425.1	s__Algoriphagus mannitolivorans	100.0	1372	1373	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_004362805.1	s__Algoriphagus boseongensis	80.1817	643	1373	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	78.3622	452	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655305.1	s__Algoriphagus sp007655305	78.3201	275	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	78.2432	440	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593605.1	s__Algoriphagus sanaruensis	78.1888	350	1373	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	77.9645	423	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583985.1	s__Algoriphagus lacus	77.8801	428	1373	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	77.6513	295	1373	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	77.5961	322	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCF_002002735.1	s__Algoriphagus sp002002735	77.5707	391	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	77.5443	232	1373	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	77.5358	220	1373	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	77.5223	268	1373	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	77.5167	342	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCF_014206875.1	s__Algoriphagus iocasae	77.3701	234	1373	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	77.2594	200	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002807035.1	s__Algoriphagus formosus	77.1456	212	1373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCA_013373065.1	s__Algoriphagus sp013373065	77.0006	206	1373	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 14:13:40,415] [INFO] GTDB search result was written to GCF_000429425.1_ASM42942v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:40,416] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:40,419] [INFO] DFAST_QC result json was written to GCF_000429425.1_ASM42942v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:40,420] [INFO] DFAST_QC completed!
[2024-01-24 14:13:40,420] [INFO] Total running time: 0h1m54s