[2024-01-24 13:40:44,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,090] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7a193a8-742d-4814-b663-dc5e5bfd6b88/dqc_reference
[2024-01-24 13:40:45,327] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,328] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,328] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5c84b99-943e-48a7-8e17-d49f4cdacfab/GCF_022549785.1_ASM2254978v1_genomic.fna.gz | prodigal -d GCF_022549785.1_ASM2254978v1_genomic.fna/cds.fna -a GCF_022549785.1_ASM2254978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:08,777] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:08,778] [INFO] Task started: HMMsearch
[2024-01-24 13:41:08,778] [INFO] Running command: hmmsearch --tblout GCF_022549785.1_ASM2254978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7a193a8-742d-4814-b663-dc5e5bfd6b88/dqc_reference/reference_markers.hmm GCF_022549785.1_ASM2254978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:09,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:09,116] [INFO] Found 6/6 markers.
[2024-01-24 13:41:09,161] [INFO] Query marker FASTA was written to GCF_022549785.1_ASM2254978v1_genomic.fna/markers.fasta
[2024-01-24 13:41:09,162] [INFO] Task started: Blastn
[2024-01-24 13:41:09,162] [INFO] Running command: blastn -query GCF_022549785.1_ASM2254978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7a193a8-742d-4814-b663-dc5e5bfd6b88/dqc_reference/reference_markers.fasta -out GCF_022549785.1_ASM2254978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:09,816] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:09,819] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:09,820] [INFO] Target genome list was writen to GCF_022549785.1_ASM2254978v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:09,836] [INFO] Task started: fastANI
[2024-01-24 13:41:09,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c84b99-943e-48a7-8e17-d49f4cdacfab/GCF_022549785.1_ASM2254978v1_genomic.fna.gz --refList GCF_022549785.1_ASM2254978v1_genomic.fna/target_genomes.txt --output GCF_022549785.1_ASM2254978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:24,205] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:24,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7a193a8-742d-4814-b663-dc5e5bfd6b88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:24,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7a193a8-742d-4814-b663-dc5e5bfd6b88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:24,223] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:24,223] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:24,223] [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
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	80.2524	639	1606	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	80.2089	610	1606	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	80.174	647	1606	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	79.0645	429	1606	95	below_threshold
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	78.7296	431	1606	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	78.5899	408	1606	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.2409	178	1606	95	below_threshold
Algoriphagus machipongonensis	strain=PR1	GCA_000166275.1	388413	388413	type	True	77.0733	122	1606	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.9591	130	1606	95	below_threshold
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	76.941	215	1606	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	76.8169	143	1606	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	76.5187	119	1606	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	76.5119	123	1606	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	76.5001	103	1606	95	below_threshold
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	76.478	99	1606	95	below_threshold
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	76.0656	98	1606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:24,225] [INFO] DFAST Taxonomy check result was written to GCF_022549785.1_ASM2254978v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:24,225] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:24,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:24,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7a193a8-742d-4814-b663-dc5e5bfd6b88/dqc_reference/checkm_data
[2024-01-24 13:41:24,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:24,276] [INFO] Task started: CheckM
[2024-01-24 13:41:24,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022549785.1_ASM2254978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022549785.1_ASM2254978v1_genomic.fna/checkm_input GCF_022549785.1_ASM2254978v1_genomic.fna/checkm_result
[2024-01-24 13:42:31,713] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:31,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:31,735] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:31,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:31,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022549785.1_ASM2254978v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:31,736] [INFO] Task started: Blastn
[2024-01-24 13:42:31,736] [INFO] Running command: blastn -query GCF_022549785.1_ASM2254978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7a193a8-742d-4814-b663-dc5e5bfd6b88/dqc_reference/reference_markers_gtdb.fasta -out GCF_022549785.1_ASM2254978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:32,558] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:32,563] [INFO] Selected 18 target genomes.
[2024-01-24 13:42:32,563] [INFO] Target genome list was writen to GCF_022549785.1_ASM2254978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:32,630] [INFO] Task started: fastANI
[2024-01-24 13:42:32,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c84b99-943e-48a7-8e17-d49f4cdacfab/GCF_022549785.1_ASM2254978v1_genomic.fna.gz --refList GCF_022549785.1_ASM2254978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022549785.1_ASM2254978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:46,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:46,399] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:46,399] [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_014637795.1	s__Belliella aquatica	80.2432	640	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	80.1979	610	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188245.1	s__Belliella buryatensis	79.0645	429	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	78.8118	245	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	78.7377	430	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014575.1	s__Cecembia rubra	77.3385	182	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	77.1547	186	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316845.1	s__Aquiflexum_A aquatile	77.1137	160	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166275.1	s__Algoriphagus machipongonensis	77.0711	122	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	76.9531	213	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	76.8859	157	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014206875.1	s__Algoriphagus iocasae	76.8338	142	1606	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	76.6025	104	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002150505.1	s__Algoriphagus ratkowskyi	76.5025	101	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
GCF_002807035.1	s__Algoriphagus formosus	76.4933	97	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCF_003254055.1	s__Algoriphagus chordae	76.485	121	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	76.4276	118	1606	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	76.3871	85	1606	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 13:42:46,401] [INFO] GTDB search result was written to GCF_022549785.1_ASM2254978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:46,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:46,407] [INFO] DFAST_QC result json was written to GCF_022549785.1_ASM2254978v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:46,407] [INFO] DFAST_QC completed!
[2024-01-24 13:42:46,407] [INFO] Total running time: 0h2m2s