[2024-01-24 12:23:50,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:50,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:50,939] [INFO] DQC Reference Directory: /var/lib/cwl/stge0441e43-852c-4cb9-87b8-3b42880439ab/dqc_reference
[2024-01-24 12:23:52,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,220] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,220] [INFO] Running command: gunzip -c /var/lib/cwl/stgb795b603-aecd-4d6c-ab0c-c9c5826e2fde/GCF_003349965.1_ASM334996v1_genomic.fna.gz | prodigal -d GCF_003349965.1_ASM334996v1_genomic.fna/cds.fna -a GCF_003349965.1_ASM334996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:15,396] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:15,397] [INFO] Task started: HMMsearch
[2024-01-24 12:24:15,397] [INFO] Running command: hmmsearch --tblout GCF_003349965.1_ASM334996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0441e43-852c-4cb9-87b8-3b42880439ab/dqc_reference/reference_markers.hmm GCF_003349965.1_ASM334996v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:15,721] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:15,722] [INFO] Found 6/6 markers.
[2024-01-24 12:24:15,770] [INFO] Query marker FASTA was written to GCF_003349965.1_ASM334996v1_genomic.fna/markers.fasta
[2024-01-24 12:24:15,771] [INFO] Task started: Blastn
[2024-01-24 12:24:15,771] [INFO] Running command: blastn -query GCF_003349965.1_ASM334996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0441e43-852c-4cb9-87b8-3b42880439ab/dqc_reference/reference_markers.fasta -out GCF_003349965.1_ASM334996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:16,356] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:16,359] [INFO] Selected 20 target genomes.
[2024-01-24 12:24:16,359] [INFO] Target genome list was writen to GCF_003349965.1_ASM334996v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:16,367] [INFO] Task started: fastANI
[2024-01-24 12:24:16,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgb795b603-aecd-4d6c-ab0c-c9c5826e2fde/GCF_003349965.1_ASM334996v1_genomic.fna.gz --refList GCF_003349965.1_ASM334996v1_genomic.fna/target_genomes.txt --output GCF_003349965.1_ASM334996v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:35,597] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:35,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0441e43-852c-4cb9-87b8-3b42880439ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:35,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0441e43-852c-4cb9-87b8-3b42880439ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:35,617] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:35,617] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:35,618] [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
Niabella yanshanensis	strain=HAMBI_3031	GCA_003349965.1	577386	577386	type	True	100.0	1826	1828	95	conclusive
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	82.0578	1251	1828	95	below_threshold
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	77.8736	376	1828	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.8261	167	1828	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	76.7598	132	1828	95	below_threshold
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	76.442	149	1828	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.327	65	1828	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	76.3209	143	1828	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	76.2657	60	1828	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	76.2296	67	1828	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	76.2296	67	1828	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	75.9988	70	1828	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	75.9953	76	1828	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	75.5123	73	1828	95	below_threshold
Chitinophaga arvensicola	strain=DSM 3695	GCA_900110835.1	29529	29529	type	True	75.4997	54	1828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:35,619] [INFO] DFAST Taxonomy check result was written to GCF_003349965.1_ASM334996v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:35,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:35,620] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:35,620] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0441e43-852c-4cb9-87b8-3b42880439ab/dqc_reference/checkm_data
[2024-01-24 12:24:35,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:35,672] [INFO] Task started: CheckM
[2024-01-24 12:24:35,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003349965.1_ASM334996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003349965.1_ASM334996v1_genomic.fna/checkm_input GCF_003349965.1_ASM334996v1_genomic.fna/checkm_result
[2024-01-24 12:25:40,214] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:40,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:40,242] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:40,242] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:40,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003349965.1_ASM334996v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:40,243] [INFO] Task started: Blastn
[2024-01-24 12:25:40,243] [INFO] Running command: blastn -query GCF_003349965.1_ASM334996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0441e43-852c-4cb9-87b8-3b42880439ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_003349965.1_ASM334996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:41,029] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:41,034] [INFO] Selected 26 target genomes.
[2024-01-24 12:25:41,034] [INFO] Target genome list was writen to GCF_003349965.1_ASM334996v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:41,054] [INFO] Task started: fastANI
[2024-01-24 12:25:41,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgb795b603-aecd-4d6c-ab0c-c9c5826e2fde/GCF_003349965.1_ASM334996v1_genomic.fna.gz --refList GCF_003349965.1_ASM334996v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003349965.1_ASM334996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:02,645] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:02,668] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:02,669] [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_003349965.1	s__Niabella yanshanensis	100.0	1826	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016719165.1	s__JJ008 sp016719165	76.8519	54	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.96	97.46	0.92	0.92	3	-
GCF_014168535.1	s__Lacibacter sp014168535	76.8069	69	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101395.1	s__Niabella drilacis	76.6445	142	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374125.1	s__Niabella aurantiaca	76.4955	149	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001896965.1	s__Niabella sp001896965	76.4622	73	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744715.1	s__Niabella sp017744715	76.4586	159	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355595.1	s__Filimonas lacunae	76.4572	67	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001654455.1	s__Niabella ginsenosidivorans	76.4341	147	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898485.1	s__46-32 sp001898485	76.4142	58	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	99.14	98.30	0.96	0.92	3	-
GCA_016710935.1	s__Ferruginibacter sp016710935	76.3373	54	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400415.1	s__JJ008 sp002400415	76.2962	68	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078015.1	s__Niastella populi	76.2657	60	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337125.1	s__Lacibacter sp002337125	76.2377	74	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464625.1	s__JJ008 sp001464625	76.2197	55	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075435.1	s__Agriterribacter sp003075435	76.1911	71	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	97.00	96.97	0.82	0.82	3	-
GCA_017744795.1	s__Niabella sp017744795	76.0795	136	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003555545.1	s__Paraflavitalea soli	75.974	68	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352145.1	s__JJ008 sp002352145	75.8602	53	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826165.1	s__JJ008 sp902826165	75.8354	82	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341975.1	s__Niastella sp004341975	75.7044	86	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017742245.1	s__Niastella sp017742245	75.5123	73	1828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:02,671] [INFO] GTDB search result was written to GCF_003349965.1_ASM334996v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:02,672] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:02,932] [INFO] DFAST_QC result json was written to GCF_003349965.1_ASM334996v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:02,932] [INFO] DFAST_QC completed!
[2024-01-24 12:26:02,932] [INFO] Total running time: 0h2m12s