[2024-01-24 14:06:29,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,507] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,507] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e87b87d-1d0f-46ca-a2d8-8edae70ccc03/dqc_reference
[2024-01-24 14:06:30,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:30,756] [INFO] Task started: Prodigal
[2024-01-24 14:06:30,757] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf3a95c3-dcb7-4e9b-907f-f67c2c5626e7/GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/cds.fna -a GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:54,462] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:54,463] [INFO] Task started: HMMsearch
[2024-01-24 14:06:54,463] [INFO] Running command: hmmsearch --tblout GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e87b87d-1d0f-46ca-a2d8-8edae70ccc03/dqc_reference/reference_markers.hmm GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:54,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:54,763] [INFO] Found 6/6 markers.
[2024-01-24 14:06:54,806] [INFO] Query marker FASTA was written to GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:54,806] [INFO] Task started: Blastn
[2024-01-24 14:06:54,806] [INFO] Running command: blastn -query GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e87b87d-1d0f-46ca-a2d8-8edae70ccc03/dqc_reference/reference_markers.fasta -out GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:55,446] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:55,450] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:55,451] [INFO] Target genome list was writen to GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:55,457] [INFO] Task started: fastANI
[2024-01-24 14:06:55,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf3a95c3-dcb7-4e9b-907f-f67c2c5626e7/GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna.gz --refList GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:08,987] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:08,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e87b87d-1d0f-46ca-a2d8-8edae70ccc03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:08,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e87b87d-1d0f-46ca-a2d8-8edae70ccc03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:09,005] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:09,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:09,006] [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 alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	100.0	1576	1580	95	conclusive
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	79.9661	803	1580	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	79.0316	641	1580	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	78.2298	428	1580	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	78.2245	549	1580	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	77.8481	479	1580	95	below_threshold
Algoriphagus oliviformis	strain=H41	GCA_017254915.1	2811231	2811231	type	True	77.772	333	1580	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	77.7268	371	1580	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	77.5379	356	1580	95	below_threshold
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	77.0984	298	1580	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	77.0056	205	1580	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	76.9921	254	1580	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	76.9747	217	1580	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:09,007] [INFO] DFAST Taxonomy check result was written to GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:07:09,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:09,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:09,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e87b87d-1d0f-46ca-a2d8-8edae70ccc03/dqc_reference/checkm_data
[2024-01-24 14:07:09,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:09,057] [INFO] Task started: CheckM
[2024-01-24 14:07:09,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/checkm_input GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:08:18,017] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:18,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:18,036] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:18,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:18,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:08:18,037] [INFO] Task started: Blastn
[2024-01-24 14:08:18,037] [INFO] Running command: blastn -query GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e87b87d-1d0f-46ca-a2d8-8edae70ccc03/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:18,890] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:18,893] [INFO] Selected 14 target genomes.
[2024-01-24 14:08:18,893] [INFO] Target genome list was writen to GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:18,903] [INFO] Task started: fastANI
[2024-01-24 14:08:18,903] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf3a95c3-dcb7-4e9b-907f-f67c2c5626e7/GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna.gz --refList GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:33,977] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:33,989] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:33,989] [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_900103735.1	s__Algoriphagus alkaliphilus	100.0	1576	1580	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	conclusive
GCF_900108085.1	s__Algoriphagus boritolerans	79.9854	801	1580	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCF_003259255.1	s__Algoriphagus litoralis	79.0241	642	1580	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	78.7836	597	1580	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	78.2272	548	1580	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	78.2224	428	1580	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	77.7167	431	1580	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	77.7091	373	1580	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	77.7075	392	1580	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	77.5295	357	1580	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	77.0984	298	1580	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	76.9934	257	1580	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	76.9712	154	1580	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.47	99.47	0.91	0.91	2	-
GCF_000429405.1	s__Algoriphagus marincola	76.7311	195	1580	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:33,990] [INFO] GTDB search result was written to GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:33,991] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:33,995] [INFO] DFAST_QC result json was written to GCF_900103735.1_IMG-taxon_2595698204_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:08:33,996] [INFO] DFAST_QC completed!
[2024-01-24 14:08:33,996] [INFO] Total running time: 0h2m4s