[2024-01-24 12:40:07,127] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,130] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,130] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd75ca0d-0ed2-4d1a-adb3-0e1dacb88512/dqc_reference
[2024-01-24 12:40:08,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,514] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,515] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf5e7278-2dc0-4c65-b81c-06f3b41ea398/GCF_003253485.1_ASM325348v1_genomic.fna.gz | prodigal -d GCF_003253485.1_ASM325348v1_genomic.fna/cds.fna -a GCF_003253485.1_ASM325348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:33,804] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:33,805] [INFO] Task started: HMMsearch
[2024-01-24 12:40:33,805] [INFO] Running command: hmmsearch --tblout GCF_003253485.1_ASM325348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd75ca0d-0ed2-4d1a-adb3-0e1dacb88512/dqc_reference/reference_markers.hmm GCF_003253485.1_ASM325348v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:34,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:34,054] [INFO] Found 6/6 markers.
[2024-01-24 12:40:34,094] [INFO] Query marker FASTA was written to GCF_003253485.1_ASM325348v1_genomic.fna/markers.fasta
[2024-01-24 12:40:34,095] [INFO] Task started: Blastn
[2024-01-24 12:40:34,095] [INFO] Running command: blastn -query GCF_003253485.1_ASM325348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd75ca0d-0ed2-4d1a-adb3-0e1dacb88512/dqc_reference/reference_markers.fasta -out GCF_003253485.1_ASM325348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:34,686] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:34,689] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:34,689] [INFO] Target genome list was writen to GCF_003253485.1_ASM325348v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:34,696] [INFO] Task started: fastANI
[2024-01-24 12:40:34,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf5e7278-2dc0-4c65-b81c-06f3b41ea398/GCF_003253485.1_ASM325348v1_genomic.fna.gz --refList GCF_003253485.1_ASM325348v1_genomic.fna/target_genomes.txt --output GCF_003253485.1_ASM325348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:49,460] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:49,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd75ca0d-0ed2-4d1a-adb3-0e1dacb88512/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:49,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd75ca0d-0ed2-4d1a-adb3-0e1dacb88512/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:49,473] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:49,473] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:49,473] [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 aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	100.0	1606	1608	95	conclusive
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	79.6908	465	1608	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	78.8473	521	1608	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	78.7067	474	1608	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	78.3706	457	1608	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	78.2979	455	1608	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	78.2013	440	1608	95	below_threshold
Algoriphagus oliviformis	strain=H41	GCA_017254915.1	2811231	2811231	type	True	77.6452	394	1608	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	77.274	281	1608	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	77.2363	253	1608	95	below_threshold
Algoriphagus resistens	strain=NH1	GCA_001442615.1	1750590	1750590	type	True	77.222	186	1608	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	77.1099	169	1608	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	76.6053	71	1608	95	below_threshold
Rhodonellum psychrophilum	strain=DSM 17998	GCA_000381545.1	336828	336828	type	True	76.2768	95	1608	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	75.9848	57	1608	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	75.7205	60	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:49,475] [INFO] DFAST Taxonomy check result was written to GCF_003253485.1_ASM325348v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:49,475] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:49,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:49,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd75ca0d-0ed2-4d1a-adb3-0e1dacb88512/dqc_reference/checkm_data
[2024-01-24 12:40:49,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:49,520] [INFO] Task started: CheckM
[2024-01-24 12:40:49,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003253485.1_ASM325348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003253485.1_ASM325348v1_genomic.fna/checkm_input GCF_003253485.1_ASM325348v1_genomic.fna/checkm_result
[2024-01-24 12:41:59,954] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:59,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:59,973] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:59,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:59,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003253485.1_ASM325348v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:59,973] [INFO] Task started: Blastn
[2024-01-24 12:41:59,974] [INFO] Running command: blastn -query GCF_003253485.1_ASM325348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd75ca0d-0ed2-4d1a-adb3-0e1dacb88512/dqc_reference/reference_markers_gtdb.fasta -out GCF_003253485.1_ASM325348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:00,709] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:00,712] [INFO] Selected 14 target genomes.
[2024-01-24 12:42:00,712] [INFO] Target genome list was writen to GCF_003253485.1_ASM325348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:00,721] [INFO] Task started: fastANI
[2024-01-24 12:42:00,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf5e7278-2dc0-4c65-b81c-06f3b41ea398/GCF_003253485.1_ASM325348v1_genomic.fna.gz --refList GCF_003253485.1_ASM325348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003253485.1_ASM325348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:12,298] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:12,310] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:12,310] [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_003253485.1	s__Algoriphagus aquaeductus	100.0	1606	1608	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_014324365.1	s__Algoriphagus sp014324365	84.7456	994	1608	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	82.5181	814	1608	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	79.6908	465	1608	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	78.8473	521	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002735.1	s__Algoriphagus sp002002735	78.6093	506	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429425.1	s__Algoriphagus mannitolivorans	78.3781	456	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362805.1	s__Algoriphagus boseongensis	78.2202	437	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429445.1	s__Algoriphagus terrigena	78.0437	421	1608	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	77.2728	281	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442615.1	s__Algoriphagus resistens	77.1907	187	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005788235.1	s__Algoriphagus sp005788235	77.0964	150	1608	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	77.0356	153	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903952135.1	s__Algoriphagus sp903952135	76.9532	237	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.47	99.47	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:12,311] [INFO] GTDB search result was written to GCF_003253485.1_ASM325348v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:12,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:12,316] [INFO] DFAST_QC result json was written to GCF_003253485.1_ASM325348v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:12,316] [INFO] DFAST_QC completed!
[2024-01-24 12:42:12,316] [INFO] Total running time: 0h2m5s