[2024-01-24 14:20:14,339] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg9274c617-9e58-446f-9284-bd3ff032c852/dqc_reference
[2024-01-24 14:20:15,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,593] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg83cdfa5b-d521-4243-8996-edcf71889531/GCF_004358035.1_ASM435803v1_genomic.fna.gz | prodigal -d GCF_004358035.1_ASM435803v1_genomic.fna/cds.fna -a GCF_004358035.1_ASM435803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:36,900] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:36,900] [INFO] Task started: HMMsearch
[2024-01-24 14:20:36,901] [INFO] Running command: hmmsearch --tblout GCF_004358035.1_ASM435803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9274c617-9e58-446f-9284-bd3ff032c852/dqc_reference/reference_markers.hmm GCF_004358035.1_ASM435803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:37,235] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:37,237] [INFO] Found 6/6 markers.
[2024-01-24 14:20:37,277] [INFO] Query marker FASTA was written to GCF_004358035.1_ASM435803v1_genomic.fna/markers.fasta
[2024-01-24 14:20:37,277] [INFO] Task started: Blastn
[2024-01-24 14:20:37,277] [INFO] Running command: blastn -query GCF_004358035.1_ASM435803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9274c617-9e58-446f-9284-bd3ff032c852/dqc_reference/reference_markers.fasta -out GCF_004358035.1_ASM435803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:37,921] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:37,924] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:37,924] [INFO] Target genome list was writen to GCF_004358035.1_ASM435803v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:37,933] [INFO] Task started: fastANI
[2024-01-24 14:20:37,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg83cdfa5b-d521-4243-8996-edcf71889531/GCF_004358035.1_ASM435803v1_genomic.fna.gz --refList GCF_004358035.1_ASM435803v1_genomic.fna/target_genomes.txt --output GCF_004358035.1_ASM435803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:55,301] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:55,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9274c617-9e58-446f-9284-bd3ff032c852/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:55,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9274c617-9e58-446f-9284-bd3ff032c852/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:55,315] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:55,315] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:20:55,315] [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 aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	100.0	1429	1430	95	inconclusive
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	97.5533	1335	1430	95	inconclusive
Algoriphagus marincola	strain=DSM 16067	GCA_000429405.1	264027	264027	type	True	93.2753	1254	1430	95	below_threshold
Algoriphagus faecimaris	strain=JCM 16561	GCA_002150585.1	686796	686796	type	True	78.6133	366	1430	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	78.4536	466	1430	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	78.2509	298	1430	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	77.7076	339	1430	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.3444	278	1430	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.3433	279	1430	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	77.2259	190	1430	95	below_threshold
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	76.7471	173	1430	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	76.4899	152	1430	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	76.476	152	1430	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.2514	79	1430	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	75.8672	57	1430	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	75.8635	58	1430	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:55,317] [INFO] DFAST Taxonomy check result was written to GCF_004358035.1_ASM435803v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:55,318] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:55,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:55,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9274c617-9e58-446f-9284-bd3ff032c852/dqc_reference/checkm_data
[2024-01-24 14:20:55,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:55,363] [INFO] Task started: CheckM
[2024-01-24 14:20:55,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358035.1_ASM435803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358035.1_ASM435803v1_genomic.fna/checkm_input GCF_004358035.1_ASM435803v1_genomic.fna/checkm_result
[2024-01-24 14:21:54,474] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:54,475] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:54,496] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:54,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:54,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358035.1_ASM435803v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:54,498] [INFO] Task started: Blastn
[2024-01-24 14:21:54,498] [INFO] Running command: blastn -query GCF_004358035.1_ASM435803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9274c617-9e58-446f-9284-bd3ff032c852/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358035.1_ASM435803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:55,263] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:55,266] [INFO] Selected 11 target genomes.
[2024-01-24 14:21:55,266] [INFO] Target genome list was writen to GCF_004358035.1_ASM435803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:55,292] [INFO] Task started: fastANI
[2024-01-24 14:21:55,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg83cdfa5b-d521-4243-8996-edcf71889531/GCF_004358035.1_ASM435803v1_genomic.fna.gz --refList GCF_004358035.1_ASM435803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358035.1_ASM435803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:05,193] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:05,206] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:05,206] [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_002807035.1	s__Algoriphagus formosus	97.5533	1335	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	conclusive
GCF_000526355.1	s__Algoriphagus marincola_A	93.5859	1169	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000429405.1	s__Algoriphagus marincola	93.2904	1253	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
GCA_013373335.1	s__Algoriphagus sp013373335	79.269	362	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373065.1	s__Algoriphagus sp013373065	78.6274	422	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101705.1	s__Algoriphagus faecimaris	78.5744	364	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_004571135.1	s__Algoriphagus kandeliae	78.4536	466	1430	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	77.7187	337	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838715.1	s__Algoriphagus sp014838715	76.8086	154	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116615.1	s__Algoriphagus locisalis	76.7471	174	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	76.476	152	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:05,209] [INFO] GTDB search result was written to GCF_004358035.1_ASM435803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:05,210] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:05,213] [INFO] DFAST_QC result json was written to GCF_004358035.1_ASM435803v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:05,213] [INFO] DFAST_QC completed!
[2024-01-24 14:22:05,214] [INFO] Total running time: 0h1m51s