[2023-06-17 16:58:56,470] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:58:56,472] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:58:56,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgc26a9c28-7f36-4df1-bb54-cca3fa183776/dqc_reference
[2023-06-17 16:58:57,774] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:58:57,775] [INFO] Task started: Prodigal
[2023-06-17 16:58:57,775] [INFO] Running command: gunzip -c /var/lib/cwl/stgc883c8b5-8418-4f58-9fa7-826dd2f0af3f/GCA_003536155.1_ASM353615v1_genomic.fna.gz | prodigal -d GCA_003536155.1_ASM353615v1_genomic.fna/cds.fna -a GCA_003536155.1_ASM353615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:59:06,514] [INFO] Task succeeded: Prodigal
[2023-06-17 16:59:06,514] [INFO] Task started: HMMsearch
[2023-06-17 16:59:06,515] [INFO] Running command: hmmsearch --tblout GCA_003536155.1_ASM353615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc26a9c28-7f36-4df1-bb54-cca3fa183776/dqc_reference/reference_markers.hmm GCA_003536155.1_ASM353615v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:59:06,794] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:59:06,796] [INFO] Found 6/6 markers.
[2023-06-17 16:59:06,819] [INFO] Query marker FASTA was written to GCA_003536155.1_ASM353615v1_genomic.fna/markers.fasta
[2023-06-17 16:59:06,820] [INFO] Task started: Blastn
[2023-06-17 16:59:06,820] [INFO] Running command: blastn -query GCA_003536155.1_ASM353615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26a9c28-7f36-4df1-bb54-cca3fa183776/dqc_reference/reference_markers.fasta -out GCA_003536155.1_ASM353615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:59:07,544] [INFO] Task succeeded: Blastn
[2023-06-17 16:59:07,555] [INFO] Selected 17 target genomes.
[2023-06-17 16:59:07,556] [INFO] Target genome list was writen to GCA_003536155.1_ASM353615v1_genomic.fna/target_genomes.txt
[2023-06-17 16:59:07,558] [INFO] Task started: fastANI
[2023-06-17 16:59:07,559] [INFO] Running command: fastANI --query /var/lib/cwl/stgc883c8b5-8418-4f58-9fa7-826dd2f0af3f/GCA_003536155.1_ASM353615v1_genomic.fna.gz --refList GCA_003536155.1_ASM353615v1_genomic.fna/target_genomes.txt --output GCA_003536155.1_ASM353615v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:59:18,193] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:18,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc26a9c28-7f36-4df1-bb54-cca3fa183776/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:59:18,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc26a9c28-7f36-4df1-bb54-cca3fa183776/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:59:18,208] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:59:18,209] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 16:59:18,209] [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 koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	79.1363	305	589	95	below_threshold
Chryseobacterium koreense	strain=CCUG 49689	GCA_001045435.1	232216	232216	type	True	79.0706	305	589	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	78.5393	271	589	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	78.5199	233	589	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	78.5144	269	589	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	78.4884	235	589	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_900112115.1	266749	266749	type	True	78.4377	286	589	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	78.4249	288	589	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	78.3988	296	589	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.8779	240	589	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	77.6861	176	589	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	77.6001	171	589	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	77.4883	175	589	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	77.3324	150	589	95	below_threshold
Chryseobacterium lacus	strain=YLOS41	GCA_003984675.1	2058346	2058346	type	True	77.3156	120	589	95	below_threshold
Chryseobacterium lacus	strain=YLOS41	GCA_003336205.1	2058346	2058346	type	True	77.3156	120	589	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 16:59:18,218] [INFO] DFAST Taxonomy check result was written to GCA_003536155.1_ASM353615v1_genomic.fna/tc_result.tsv
[2023-06-17 16:59:18,219] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:59:18,219] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:59:18,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc26a9c28-7f36-4df1-bb54-cca3fa183776/dqc_reference/checkm_data
[2023-06-17 16:59:18,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:59:18,248] [INFO] Task started: CheckM
[2023-06-17 16:59:18,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003536155.1_ASM353615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003536155.1_ASM353615v1_genomic.fna/checkm_input GCA_003536155.1_ASM353615v1_genomic.fna/checkm_result
[2023-06-17 16:59:47,997] [INFO] Task succeeded: CheckM
[2023-06-17 16:59:47,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:59:48,021] [INFO] ===== Completeness check finished =====
[2023-06-17 16:59:48,021] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:59:48,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003536155.1_ASM353615v1_genomic.fna/markers.fasta)
[2023-06-17 16:59:48,022] [INFO] Task started: Blastn
[2023-06-17 16:59:48,022] [INFO] Running command: blastn -query GCA_003536155.1_ASM353615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26a9c28-7f36-4df1-bb54-cca3fa183776/dqc_reference/reference_markers_gtdb.fasta -out GCA_003536155.1_ASM353615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:59:48,885] [INFO] Task succeeded: Blastn
[2023-06-17 16:59:48,890] [INFO] Selected 15 target genomes.
[2023-06-17 16:59:48,891] [INFO] Target genome list was writen to GCA_003536155.1_ASM353615v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:59:48,904] [INFO] Task started: fastANI
[2023-06-17 16:59:48,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgc883c8b5-8418-4f58-9fa7-826dd2f0af3f/GCA_003536155.1_ASM353615v1_genomic.fna.gz --refList GCA_003536155.1_ASM353615v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003536155.1_ASM353615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:59:56,716] [INFO] Task succeeded: fastANI
[2023-06-17 16:59:56,733] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 16:59:56,733] [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_002426785.1	s__Kaistella sp002426785	97.9633	497	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	conclusive
GCF_001403755.1	s__Kaistella senegalense	79.7738	285	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735695.2	s__Kaistella haifensis	79.3436	289	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.72	96.43	0.83	0.82	4	-
GCF_002205795.1	s__Kaistella sp002205795	79.2954	248	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	95.66	95.02	0.89	0.88	3	-
GCF_001045435.1	s__Kaistella koreensis	79.0706	305	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.98	99.98	0.99	0.99	2	-
GCA_018902795.1	s__Kaistella sp018902795	78.6511	301	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453895.1	s__Kaistella sp002453895	78.6258	250	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900156725.1	s__Kaistella chaponensis	78.5513	270	589	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	78.5199	233	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002197835.1	s__Kaistella sp002197835	78.4957	279	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.62	97.62	0.94	0.94	2	-
GCA_015999765.1	s__Kaistella sp015999765	78.4572	235	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCF_000812865.1	s__Kaistella jeonii	78.4379	287	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	99.99	1.00	1.00	3	-
GCF_008014695.1	s__Kaistella sp008014695	77.8998	177	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860585.1	s__Kaistella carnis	77.8779	240	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.44	0.91	0.90	4	-
GCF_900143185.1	s__Chryseobacterium scophthalmum	77.6001	171	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.42	95.16	0.86	0.85	5	-
--------------------------------------------------------------------------------
[2023-06-17 16:59:56,735] [INFO] GTDB search result was written to GCA_003536155.1_ASM353615v1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:59:56,736] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:59:56,740] [INFO] DFAST_QC result json was written to GCA_003536155.1_ASM353615v1_genomic.fna/dqc_result.json
[2023-06-17 16:59:56,740] [INFO] DFAST_QC completed!
[2023-06-17 16:59:56,740] [INFO] Total running time: 0h1m0s