[2023-06-19 00:58:10,214] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:58:10,230] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:58:10,231] [INFO] DQC Reference Directory: /var/lib/cwl/stgc725d0f9-c73e-4d0c-a314-f3c49bc93e46/dqc_reference
[2023-06-19 00:58:12,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:58:12,543] [INFO] Task started: Prodigal
[2023-06-19 00:58:12,543] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2c5d82a-385c-49ab-96ad-cd8f182d15ba/GCA_018267575.1_ASM1826757v1_genomic.fna.gz | prodigal -d GCA_018267575.1_ASM1826757v1_genomic.fna/cds.fna -a GCA_018267575.1_ASM1826757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:58:38,177] [INFO] Task succeeded: Prodigal
[2023-06-19 00:58:38,177] [INFO] Task started: HMMsearch
[2023-06-19 00:58:38,177] [INFO] Running command: hmmsearch --tblout GCA_018267575.1_ASM1826757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc725d0f9-c73e-4d0c-a314-f3c49bc93e46/dqc_reference/reference_markers.hmm GCA_018267575.1_ASM1826757v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:58:38,415] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:58:38,416] [INFO] Found 6/6 markers.
[2023-06-19 00:58:38,460] [INFO] Query marker FASTA was written to GCA_018267575.1_ASM1826757v1_genomic.fna/markers.fasta
[2023-06-19 00:58:38,460] [INFO] Task started: Blastn
[2023-06-19 00:58:38,460] [INFO] Running command: blastn -query GCA_018267575.1_ASM1826757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc725d0f9-c73e-4d0c-a314-f3c49bc93e46/dqc_reference/reference_markers.fasta -out GCA_018267575.1_ASM1826757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:58:39,092] [INFO] Task succeeded: Blastn
[2023-06-19 00:58:39,100] [INFO] Selected 25 target genomes.
[2023-06-19 00:58:39,100] [INFO] Target genome list was writen to GCA_018267575.1_ASM1826757v1_genomic.fna/target_genomes.txt
[2023-06-19 00:58:39,103] [INFO] Task started: fastANI
[2023-06-19 00:58:39,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c5d82a-385c-49ab-96ad-cd8f182d15ba/GCA_018267575.1_ASM1826757v1_genomic.fna.gz --refList GCA_018267575.1_ASM1826757v1_genomic.fna/target_genomes.txt --output GCA_018267575.1_ASM1826757v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:59:01,486] [INFO] Task succeeded: fastANI
[2023-06-19 00:59:01,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc725d0f9-c73e-4d0c-a314-f3c49bc93e46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:59:01,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc725d0f9-c73e-4d0c-a314-f3c49bc93e46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:59:01,497] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:59:01,498] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:59:01,498] [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
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	75.8885	66	1597	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.8399	53	1597	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	75.8016	61	1597	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	75.7311	77	1597	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	75.7116	73	1597	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.7064	75	1597	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	75.6656	80	1597	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	75.5647	65	1597	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	75.4829	63	1597	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	75.4632	62	1597	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	75.4594	57	1597	95	below_threshold
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	75.336	55	1597	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.2629	78	1597	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:59:01,501] [INFO] DFAST Taxonomy check result was written to GCA_018267575.1_ASM1826757v1_genomic.fna/tc_result.tsv
[2023-06-19 00:59:01,501] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:59:01,501] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:59:01,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc725d0f9-c73e-4d0c-a314-f3c49bc93e46/dqc_reference/checkm_data
[2023-06-19 00:59:01,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:59:01,547] [INFO] Task started: CheckM
[2023-06-19 00:59:01,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018267575.1_ASM1826757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018267575.1_ASM1826757v1_genomic.fna/checkm_input GCA_018267575.1_ASM1826757v1_genomic.fna/checkm_result
[2023-06-19 01:00:12,225] [INFO] Task succeeded: CheckM
[2023-06-19 01:00:12,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:00:12,249] [INFO] ===== Completeness check finished =====
[2023-06-19 01:00:12,250] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:00:12,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018267575.1_ASM1826757v1_genomic.fna/markers.fasta)
[2023-06-19 01:00:12,250] [INFO] Task started: Blastn
[2023-06-19 01:00:12,250] [INFO] Running command: blastn -query GCA_018267575.1_ASM1826757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc725d0f9-c73e-4d0c-a314-f3c49bc93e46/dqc_reference/reference_markers_gtdb.fasta -out GCA_018267575.1_ASM1826757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:00:13,225] [INFO] Task succeeded: Blastn
[2023-06-19 01:00:13,228] [INFO] Selected 25 target genomes.
[2023-06-19 01:00:13,228] [INFO] Target genome list was writen to GCA_018267575.1_ASM1826757v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:00:13,240] [INFO] Task started: fastANI
[2023-06-19 01:00:13,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c5d82a-385c-49ab-96ad-cd8f182d15ba/GCA_018267575.1_ASM1826757v1_genomic.fna.gz --refList GCA_018267575.1_ASM1826757v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018267575.1_ASM1826757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:00:32,968] [INFO] Task succeeded: fastANI
[2023-06-19 01:00:32,981] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:00:32,981] [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_018267575.1	s__Puia sp018267575	100.0	1591	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001302245.1	s__PMP191F sp001302245	76.8751	83	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCA_018266575.1	s__Puia sp018266575	76.4612	163	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266455.1	s__Puia sp018266455	76.2834	177	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927975.1	s__Puia sp903927975	76.2561	198	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	99.89	99.89	0.91	0.91	2	-
GCA_013288945.1	s__Puia sp013288945	75.9988	96	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200915.1	s__AWTP1-9 sp016200915	75.9901	68	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	99.92	99.92	0.98	0.98	2	-
GCA_001898505.1	s__Puia sp001898505	75.8817	64	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903906365.1	s__Puia sp903906365	75.8459	85	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	99.91	99.90	0.99	0.98	4	-
GCA_018267615.1	s__Puia sp018267615	75.7878	108	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003555545.1	s__Paraflavitalea soli	75.7812	60	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759375.1	s__Paraflavitalea devenefica	75.6629	78	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011357845.1	s__UBA3961 sp011357845	75.655	67	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA3961	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118265.1	s__Lacibacter luteus	75.4748	63	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703625.1	s__Ferruginibacter sp016703625	75.4031	50	1597	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	97.77	96.12	0.94	0.91	5	-
--------------------------------------------------------------------------------
[2023-06-19 01:00:32,984] [INFO] GTDB search result was written to GCA_018267575.1_ASM1826757v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:00:32,984] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:00:32,991] [INFO] DFAST_QC result json was written to GCA_018267575.1_ASM1826757v1_genomic.fna/dqc_result.json
[2023-06-19 01:00:32,991] [INFO] DFAST_QC completed!
[2023-06-19 01:00:32,991] [INFO] Total running time: 0h2m23s