[2024-01-24 12:37:23,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:23,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:23,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c704b52-ed50-4bcd-9ee1-0c99a514ea22/dqc_reference
[2024-01-24 12:37:24,880] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:24,881] [INFO] Task started: Prodigal
[2024-01-24 12:37:24,882] [INFO] Running command: gunzip -c /var/lib/cwl/stge3123c46-270c-4f27-a84c-94ad94231b5c/GCF_002023715.1_ASM202371v1_genomic.fna.gz | prodigal -d GCF_002023715.1_ASM202371v1_genomic.fna/cds.fna -a GCF_002023715.1_ASM202371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:38,755] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:38,756] [INFO] Task started: HMMsearch
[2024-01-24 12:37:38,756] [INFO] Running command: hmmsearch --tblout GCF_002023715.1_ASM202371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c704b52-ed50-4bcd-9ee1-0c99a514ea22/dqc_reference/reference_markers.hmm GCF_002023715.1_ASM202371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:39,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:39,054] [INFO] Found 6/6 markers.
[2024-01-24 12:37:39,089] [INFO] Query marker FASTA was written to GCF_002023715.1_ASM202371v1_genomic.fna/markers.fasta
[2024-01-24 12:37:39,089] [INFO] Task started: Blastn
[2024-01-24 12:37:39,089] [INFO] Running command: blastn -query GCF_002023715.1_ASM202371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c704b52-ed50-4bcd-9ee1-0c99a514ea22/dqc_reference/reference_markers.fasta -out GCF_002023715.1_ASM202371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:39,722] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:39,725] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:39,726] [INFO] Target genome list was writen to GCF_002023715.1_ASM202371v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:39,733] [INFO] Task started: fastANI
[2024-01-24 12:37:39,734] [INFO] Running command: fastANI --query /var/lib/cwl/stge3123c46-270c-4f27-a84c-94ad94231b5c/GCF_002023715.1_ASM202371v1_genomic.fna.gz --refList GCF_002023715.1_ASM202371v1_genomic.fna/target_genomes.txt --output GCF_002023715.1_ASM202371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:49,948] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:49,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c704b52-ed50-4bcd-9ee1-0c99a514ea22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:49,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c704b52-ed50-4bcd-9ee1-0c99a514ea22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:49,959] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:49,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:49,960] [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
Elizabethkingia occulta	strain=G4070	GCA_002023715.1	1867263	1867263	type	True	100.0	1374	1375	95	conclusive
Elizabethkingia ursingii	strain=G4122	GCA_001521765.1	1756150	1756150	type	True	94.7686	1166	1375	95	below_threshold
Elizabethkingia miricola	strain=DSM 14571	GCA_008124555.1	172045	172045	type	True	91.3473	1139	1375	95	below_threshold
Elizabethkingia miricola	strain=GTC_862	GCA_001675285.1	172045	172045	type	True	91.284	1150	1375	95	below_threshold
Elizabethkingia bruuniana	strain=G0146	GCA_002024805.1	1756149	1756149	type	True	91.2489	1145	1375	95	below_threshold
Elizabethkingia bruuniana	strain=G0146	GCA_002023205.1	1756149	1756149	type	True	91.2284	1153	1375	95	below_threshold
Elizabethkingia anophelis	strain=R26	GCA_002023665.2	1117645	1117645	type	True	90.5101	1123	1375	95	below_threshold
Elizabethkingia anophelis		GCA_017124975.1	1117645	1117645	type	True	90.4368	1115	1375	95	below_threshold
Elizabethkingia anophelis	strain=R26	GCA_000331815.1	1117645	1117645	type	True	90.4359	1129	1375	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.4171	86	1375	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.3835	87	1375	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	76.9547	98	1375	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:49,961] [INFO] DFAST Taxonomy check result was written to GCF_002023715.1_ASM202371v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:49,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:49,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:49,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c704b52-ed50-4bcd-9ee1-0c99a514ea22/dqc_reference/checkm_data
[2024-01-24 12:37:49,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:50,002] [INFO] Task started: CheckM
[2024-01-24 12:37:50,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002023715.1_ASM202371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002023715.1_ASM202371v1_genomic.fna/checkm_input GCF_002023715.1_ASM202371v1_genomic.fna/checkm_result
[2024-01-24 12:38:32,667] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:32,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:32,686] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:32,687] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:32,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002023715.1_ASM202371v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:32,688] [INFO] Task started: Blastn
[2024-01-24 12:38:32,688] [INFO] Running command: blastn -query GCF_002023715.1_ASM202371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c704b52-ed50-4bcd-9ee1-0c99a514ea22/dqc_reference/reference_markers_gtdb.fasta -out GCF_002023715.1_ASM202371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:33,558] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:33,562] [INFO] Selected 6 target genomes.
[2024-01-24 12:38:33,562] [INFO] Target genome list was writen to GCF_002023715.1_ASM202371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:33,568] [INFO] Task started: fastANI
[2024-01-24 12:38:33,568] [INFO] Running command: fastANI --query /var/lib/cwl/stge3123c46-270c-4f27-a84c-94ad94231b5c/GCF_002023715.1_ASM202371v1_genomic.fna.gz --refList GCF_002023715.1_ASM202371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002023715.1_ASM202371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:40,367] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:40,379] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:40,379] [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_002023715.1	s__Elizabethkingia occulta	100.0	1374	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	99.55	99.55	0.94	0.94	2	conclusive
GCF_001521765.1	s__Elizabethkingia ursingii	94.7793	1165	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.28	97.02	0.89	0.88	5	-
GCF_003058195.1	s__Elizabethkingia sp003058195	92.5845	1116	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001675285.1	s__Elizabethkingia miricola	91.284	1150	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.66	96.19	0.91	0.86	23	-
GCF_002024805.1	s__Elizabethkingia bruuniana	91.254	1144	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.72	96.90	0.94	0.86	13	-
GCF_002023665.2	s__Elizabethkingia anophelis	90.5101	1123	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	98.27	97.37	0.90	0.86	104	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:40,381] [INFO] GTDB search result was written to GCF_002023715.1_ASM202371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:40,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:40,384] [INFO] DFAST_QC result json was written to GCF_002023715.1_ASM202371v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:40,384] [INFO] DFAST_QC completed!
[2024-01-24 12:38:40,384] [INFO] Total running time: 0h1m17s