[2024-01-24 14:13:17,336] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:17,337] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:17,338] [INFO] DQC Reference Directory: /var/lib/cwl/stg32867c92-5668-4e30-b0e5-637fe93642ba/dqc_reference
[2024-01-24 14:13:18,667] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:18,668] [INFO] Task started: Prodigal
[2024-01-24 14:13:18,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg40b8ef30-7602-4c82-a9bb-2272d6343843/GCF_022549775.1_ASM2254977v1_genomic.fna.gz | prodigal -d GCF_022549775.1_ASM2254977v1_genomic.fna/cds.fna -a GCF_022549775.1_ASM2254977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:40,866] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:40,866] [INFO] Task started: HMMsearch
[2024-01-24 14:13:40,867] [INFO] Running command: hmmsearch --tblout GCF_022549775.1_ASM2254977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32867c92-5668-4e30-b0e5-637fe93642ba/dqc_reference/reference_markers.hmm GCF_022549775.1_ASM2254977v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:41,206] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:41,208] [INFO] Found 6/6 markers.
[2024-01-24 14:13:41,262] [INFO] Query marker FASTA was written to GCF_022549775.1_ASM2254977v1_genomic.fna/markers.fasta
[2024-01-24 14:13:41,263] [INFO] Task started: Blastn
[2024-01-24 14:13:41,263] [INFO] Running command: blastn -query GCF_022549775.1_ASM2254977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32867c92-5668-4e30-b0e5-637fe93642ba/dqc_reference/reference_markers.fasta -out GCF_022549775.1_ASM2254977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:41,887] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:41,890] [INFO] Selected 16 target genomes.
[2024-01-24 14:13:41,891] [INFO] Target genome list was writen to GCF_022549775.1_ASM2254977v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:41,900] [INFO] Task started: fastANI
[2024-01-24 14:13:41,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b8ef30-7602-4c82-a9bb-2272d6343843/GCF_022549775.1_ASM2254977v1_genomic.fna.gz --refList GCF_022549775.1_ASM2254977v1_genomic.fna/target_genomes.txt --output GCF_022549775.1_ASM2254977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:54,663] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:54,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32867c92-5668-4e30-b0e5-637fe93642ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:54,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32867c92-5668-4e30-b0e5-637fe93642ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:54,683] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:54,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:54,684] [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 kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	86.8957	1048	1619	95	below_threshold
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	78.7615	375	1619	95	below_threshold
Belliella buryatensis	strain=5C	GCA_900188245.1	1500549	1500549	type	True	78.2858	363	1619	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	78.0905	151	1619	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	78.0457	295	1619	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	77.9578	294	1619	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	77.902	330	1619	95	below_threshold
Echinicola pacifica	strain=DSM 19836	GCA_000373245.1	346377	346377	type	True	76.8965	84	1619	95	below_threshold
Echinicola pacifica	strain=KCTC 12368	GCA_014651455.1	346377	346377	type	True	76.8597	86	1619	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	76.7085	139	1619	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.6202	103	1619	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	76.5257	90	1619	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_003254355.1	57028	57028	type	True	76.4836	93	1619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:54,687] [INFO] DFAST Taxonomy check result was written to GCF_022549775.1_ASM2254977v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:54,688] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:54,688] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:54,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32867c92-5668-4e30-b0e5-637fe93642ba/dqc_reference/checkm_data
[2024-01-24 14:13:54,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:54,747] [INFO] Task started: CheckM
[2024-01-24 14:13:54,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022549775.1_ASM2254977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022549775.1_ASM2254977v1_genomic.fna/checkm_input GCF_022549775.1_ASM2254977v1_genomic.fna/checkm_result
[2024-01-24 14:14:57,363] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:57,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:57,388] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:57,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:57,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022549775.1_ASM2254977v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:57,389] [INFO] Task started: Blastn
[2024-01-24 14:14:57,389] [INFO] Running command: blastn -query GCF_022549775.1_ASM2254977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32867c92-5668-4e30-b0e5-637fe93642ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_022549775.1_ASM2254977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:58,158] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:58,163] [INFO] Selected 22 target genomes.
[2024-01-24 14:14:58,163] [INFO] Target genome list was writen to GCF_022549775.1_ASM2254977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:58,184] [INFO] Task started: fastANI
[2024-01-24 14:14:58,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg40b8ef30-7602-4c82-a9bb-2272d6343843/GCF_022549775.1_ASM2254977v1_genomic.fna.gz --refList GCF_022549775.1_ASM2254977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022549775.1_ASM2254977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:13,199] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:13,218] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:15:13,218] [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_900156785.1	s__Belliella pelovolcani	78.7612	375	1619	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	78.2855	363	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	77.9696	293	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652135.1	s__Mongoliitalea lutea	77.9202	157	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	77.8849	331	1619	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	76.9693	169	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	76.965	144	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373245.1	s__Echinicola pacifica	76.8965	84	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015533855.1	s__Echinicola sp015533855	76.8438	111	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	76.6929	140	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	76.64	93	1619	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	76.6341	75	1619	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	76.6202	103	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	76.6	106	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002150505.1	s__Algoriphagus ratkowskyi	76.5257	90	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
GCF_900115305.1	s__Algoriphagus ornithinivorans	76.4433	103	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
GCF_001050135.1	s__Cyclobacterium amurskyense	76.1771	78	1619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:13,220] [INFO] GTDB search result was written to GCF_022549775.1_ASM2254977v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:13,220] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:13,224] [INFO] DFAST_QC result json was written to GCF_022549775.1_ASM2254977v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:13,224] [INFO] DFAST_QC completed!
[2024-01-24 14:15:13,224] [INFO] Total running time: 0h1m56s