[2024-01-24 13:32:41,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f764873-8646-4c6a-a53d-0d1528160cd1/dqc_reference
[2024-01-24 13:32:42,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,577] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dd1f1f0-777d-41c5-9a62-d7e9c40751ef/GCF_019038595.1_ASM1903859v1_genomic.fna.gz | prodigal -d GCF_019038595.1_ASM1903859v1_genomic.fna/cds.fna -a GCF_019038595.1_ASM1903859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:55,252] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:55,253] [INFO] Task started: HMMsearch
[2024-01-24 13:32:55,253] [INFO] Running command: hmmsearch --tblout GCF_019038595.1_ASM1903859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f764873-8646-4c6a-a53d-0d1528160cd1/dqc_reference/reference_markers.hmm GCF_019038595.1_ASM1903859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:55,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:55,533] [INFO] Found 6/6 markers.
[2024-01-24 13:32:55,568] [INFO] Query marker FASTA was written to GCF_019038595.1_ASM1903859v1_genomic.fna/markers.fasta
[2024-01-24 13:32:55,568] [INFO] Task started: Blastn
[2024-01-24 13:32:55,569] [INFO] Running command: blastn -query GCF_019038595.1_ASM1903859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f764873-8646-4c6a-a53d-0d1528160cd1/dqc_reference/reference_markers.fasta -out GCF_019038595.1_ASM1903859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:56,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:56,289] [INFO] Selected 21 target genomes.
[2024-01-24 13:32:56,289] [INFO] Target genome list was writen to GCF_019038595.1_ASM1903859v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:56,306] [INFO] Task started: fastANI
[2024-01-24 13:32:56,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd1f1f0-777d-41c5-9a62-d7e9c40751ef/GCF_019038595.1_ASM1903859v1_genomic.fna.gz --refList GCF_019038595.1_ASM1903859v1_genomic.fna/target_genomes.txt --output GCF_019038595.1_ASM1903859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:11,267] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:11,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f764873-8646-4c6a-a53d-0d1528160cd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:11,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f764873-8646-4c6a-a53d-0d1528160cd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:11,284] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:11,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:11,285] [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
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	82.4917	560	1022	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	82.4782	561	1022	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	78.7488	387	1022	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	78.7392	381	1022	95	below_threshold
Kaistella treverensis	strain=DSM 22251	GCA_900114045.1	631455	631455	type	True	78.7316	322	1022	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	78.7121	393	1022	95	below_threshold
Chryseobacterium koreense	strain=CCUG 49689	GCA_001045435.1	232216	232216	type	True	78.4377	317	1022	95	below_threshold
Kaistella solincola	strain=DSM 22468	GCA_000812875.1	510955	510955	type	True	78.4167	299	1022	95	below_threshold
Chryseobacterium koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	78.391	317	1022	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	78.3421	334	1022	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	78.2601	347	1022	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	78.124	304	1022	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	77.9144	246	1022	95	below_threshold
Chryseobacterium echinoideorum	strain=CC-CZW010	GCA_007474535.1	1549648	1549648	type	True	77.5422	228	1022	95	below_threshold
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	77.5357	206	1022	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	77.4125	229	1022	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	77.4104	196	1022	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	77.3893	206	1022	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	77.3799	225	1022	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	77.3095	221	1022	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	77.2142	235	1022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,288] [INFO] DFAST Taxonomy check result was written to GCF_019038595.1_ASM1903859v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:11,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:11,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:11,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f764873-8646-4c6a-a53d-0d1528160cd1/dqc_reference/checkm_data
[2024-01-24 13:33:11,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:11,343] [INFO] Task started: CheckM
[2024-01-24 13:33:11,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019038595.1_ASM1903859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019038595.1_ASM1903859v1_genomic.fna/checkm_input GCF_019038595.1_ASM1903859v1_genomic.fna/checkm_result
[2024-01-24 13:33:52,643] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:52,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:52,667] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:52,667] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:52,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019038595.1_ASM1903859v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:52,668] [INFO] Task started: Blastn
[2024-01-24 13:33:52,668] [INFO] Running command: blastn -query GCF_019038595.1_ASM1903859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f764873-8646-4c6a-a53d-0d1528160cd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019038595.1_ASM1903859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:53,571] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:53,575] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:53,575] [INFO] Target genome list was writen to GCF_019038595.1_ASM1903859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:54,271] [INFO] Task started: fastANI
[2024-01-24 13:33:54,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd1f1f0-777d-41c5-9a62-d7e9c40751ef/GCF_019038595.1_ASM1903859v1_genomic.fna.gz --refList GCF_019038595.1_ASM1903859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019038595.1_ASM1903859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:00,725] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:00,737] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:00,738] [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
GCA_002197835.1	s__Kaistella sp002197835	97.6227	881	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.62	97.62	0.94	0.94	2	conclusive
GCA_018902795.1	s__Kaistella sp018902795	91.7823	847	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019195395.1	s__Kaistella sp019195395	82.4703	562	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015999765.1	s__Kaistella sp015999765	81.9091	564	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCA_002453895.1	s__Kaistella sp002453895	81.8426	572	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002205795.1	s__Kaistella sp002205795	80.4838	556	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	95.66	95.02	0.89	0.88	3	-
GCF_900156725.1	s__Kaistella chaponensis	78.7616	379	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426785.1	s__Kaistella sp002426785	78.6922	324	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
GCA_000023725.1	s__Kaistella sp000023725	78.6214	385	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003669035.1	s__Chryseobacterium sp003669035	77.4502	215	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:00,740] [INFO] GTDB search result was written to GCF_019038595.1_ASM1903859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:00,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:00,745] [INFO] DFAST_QC result json was written to GCF_019038595.1_ASM1903859v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:00,745] [INFO] DFAST_QC completed!
[2024-01-24 13:34:00,745] [INFO] Total running time: 0h1m19s