[2024-01-24 11:51:24,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,585] [INFO] DQC Reference Directory: /var/lib/cwl/stgbece298d-8f01-441c-9fe4-a4b5fce6c31c/dqc_reference
[2024-01-24 11:51:25,840] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,840] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,841] [INFO] Running command: gunzip -c /var/lib/cwl/stg247ca0d3-4ecd-425d-9d04-9c4bbe4ce885/GCF_014623485.1_ASM1462348v1_genomic.fna.gz | prodigal -d GCF_014623485.1_ASM1462348v1_genomic.fna/cds.fna -a GCF_014623485.1_ASM1462348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:38,736] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:38,737] [INFO] Task started: HMMsearch
[2024-01-24 11:51:38,737] [INFO] Running command: hmmsearch --tblout GCF_014623485.1_ASM1462348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbece298d-8f01-441c-9fe4-a4b5fce6c31c/dqc_reference/reference_markers.hmm GCF_014623485.1_ASM1462348v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:38,993] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:38,994] [INFO] Found 6/6 markers.
[2024-01-24 11:51:39,028] [INFO] Query marker FASTA was written to GCF_014623485.1_ASM1462348v1_genomic.fna/markers.fasta
[2024-01-24 11:51:39,029] [INFO] Task started: Blastn
[2024-01-24 11:51:39,029] [INFO] Running command: blastn -query GCF_014623485.1_ASM1462348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbece298d-8f01-441c-9fe4-a4b5fce6c31c/dqc_reference/reference_markers.fasta -out GCF_014623485.1_ASM1462348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:39,698] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:39,702] [INFO] Selected 19 target genomes.
[2024-01-24 11:51:39,703] [INFO] Target genome list was writen to GCF_014623485.1_ASM1462348v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:39,712] [INFO] Task started: fastANI
[2024-01-24 11:51:39,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg247ca0d3-4ecd-425d-9d04-9c4bbe4ce885/GCF_014623485.1_ASM1462348v1_genomic.fna.gz --refList GCF_014623485.1_ASM1462348v1_genomic.fna/target_genomes.txt --output GCF_014623485.1_ASM1462348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:51,226] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:51,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbece298d-8f01-441c-9fe4-a4b5fce6c31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:51,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbece298d-8f01-441c-9fe4-a4b5fce6c31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:51,240] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:51,240] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:51,241] [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	80.0599	420	981	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	80.0009	423	981	95	below_threshold
Chryseobacterium koreense	strain=DSM 25209	GCA_014201785.1	232216	232216	type	True	78.6903	308	981	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	78.6775	375	981	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	78.676	316	981	95	below_threshold
Chryseobacterium koreense	strain=CCUG 49689	GCA_001045435.1	232216	232216	type	True	78.6488	312	981	95	below_threshold
Kaistella treverensis	strain=DSM 22251	GCA_900114045.1	631455	631455	type	True	78.5644	282	981	95	below_threshold
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	78.4766	355	981	95	below_threshold
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	78.3662	351	981	95	below_threshold
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	78.2017	349	981	95	below_threshold
Kaistella solincola	strain=DSM 22468	GCA_000812875.1	510955	510955	type	True	78.1139	274	981	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	78.0193	242	981	95	below_threshold
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	77.6351	243	981	95	below_threshold
Chryseobacterium glaciei	strain=IHBB 10212	GCA_001648155.1	1685010	1685010	type	True	77.5837	203	981	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	77.4966	228	981	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	77.4412	165	981	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	77.4129	156	981	95	below_threshold
Chryseobacterium caseinilyticum	strain=GCR10	GCA_014837145.1	2771428	2771428	type	True	77.2552	197	981	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:51,242] [INFO] DFAST Taxonomy check result was written to GCF_014623485.1_ASM1462348v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:51,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:51,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:51,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbece298d-8f01-441c-9fe4-a4b5fce6c31c/dqc_reference/checkm_data
[2024-01-24 11:51:51,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:51,274] [INFO] Task started: CheckM
[2024-01-24 11:51:51,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014623485.1_ASM1462348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014623485.1_ASM1462348v1_genomic.fna/checkm_input GCF_014623485.1_ASM1462348v1_genomic.fna/checkm_result
[2024-01-24 11:52:32,937] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:32,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:32,963] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:32,963] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:32,964] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014623485.1_ASM1462348v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:32,964] [INFO] Task started: Blastn
[2024-01-24 11:52:32,964] [INFO] Running command: blastn -query GCF_014623485.1_ASM1462348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbece298d-8f01-441c-9fe4-a4b5fce6c31c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014623485.1_ASM1462348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:33,834] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:33,838] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:33,839] [INFO] Target genome list was writen to GCF_014623485.1_ASM1462348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:33,850] [INFO] Task started: fastANI
[2024-01-24 11:52:33,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg247ca0d3-4ecd-425d-9d04-9c4bbe4ce885/GCF_014623485.1_ASM1462348v1_genomic.fna.gz --refList GCF_014623485.1_ASM1462348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014623485.1_ASM1462348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:41,612] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:41,624] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:41,624] [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_000735695.2	s__Kaistella haifensis	96.4072	748	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.72	96.43	0.83	0.82	4	conclusive
GCF_001403755.1	s__Kaistella senegalense	91.9475	700	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205795.1	s__Kaistella sp002205795	81.8984	461	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	95.66	95.02	0.89	0.88	3	-
GCA_002453895.1	s__Kaistella sp002453895	80.3841	461	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002197835.1	s__Kaistella sp002197835	80.3279	462	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	97.62	97.62	0.94	0.94	2	-
GCA_018902795.1	s__Kaistella sp018902795	80.1852	490	981	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	80.1259	408	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCF_019195395.1	s__Kaistella sp019195395	80.0142	422	981	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	79.2341	342	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
GCF_900156725.1	s__Kaistella chaponensis	78.6919	372	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045435.1	s__Kaistella koreensis	78.6831	309	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	99.98	99.98	0.99	0.99	2	-
GCF_000812865.1	s__Kaistella jeonii	78.3662	351	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	99.99	1.00	1.00	3	-
GCF_015679325.1	s__Kaistella gelatinilytica	78.2012	349	981	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:41,626] [INFO] GTDB search result was written to GCF_014623485.1_ASM1462348v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:41,627] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:41,634] [INFO] DFAST_QC result json was written to GCF_014623485.1_ASM1462348v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:41,634] [INFO] DFAST_QC completed!
[2024-01-24 11:52:41,634] [INFO] Total running time: 0h1m17s