[2024-01-24 13:09:28,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:28,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:28,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg52093f74-b397-4877-b161-5e7d0da650d1/dqc_reference
[2024-01-24 13:09:29,726] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:29,727] [INFO] Task started: Prodigal
[2024-01-24 13:09:29,727] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ed338a0-cb1d-4e51-889a-57b68594c624/GCF_000374045.1_ASM37404v1_genomic.fna.gz | prodigal -d GCF_000374045.1_ASM37404v1_genomic.fna/cds.fna -a GCF_000374045.1_ASM37404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:52,323] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:52,324] [INFO] Task started: HMMsearch
[2024-01-24 13:09:52,324] [INFO] Running command: hmmsearch --tblout GCF_000374045.1_ASM37404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52093f74-b397-4877-b161-5e7d0da650d1/dqc_reference/reference_markers.hmm GCF_000374045.1_ASM37404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:52,704] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:52,706] [INFO] Found 6/6 markers.
[2024-01-24 13:09:52,755] [INFO] Query marker FASTA was written to GCF_000374045.1_ASM37404v1_genomic.fna/markers.fasta
[2024-01-24 13:09:52,755] [INFO] Task started: Blastn
[2024-01-24 13:09:52,755] [INFO] Running command: blastn -query GCF_000374045.1_ASM37404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52093f74-b397-4877-b161-5e7d0da650d1/dqc_reference/reference_markers.fasta -out GCF_000374045.1_ASM37404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:53,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:53,340] [INFO] Selected 22 target genomes.
[2024-01-24 13:09:53,341] [INFO] Target genome list was writen to GCF_000374045.1_ASM37404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:53,350] [INFO] Task started: fastANI
[2024-01-24 13:09:53,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed338a0-cb1d-4e51-889a-57b68594c624/GCF_000374045.1_ASM37404v1_genomic.fna.gz --refList GCF_000374045.1_ASM37404v1_genomic.fna/target_genomes.txt --output GCF_000374045.1_ASM37404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:11,999] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:11,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52093f74-b397-4877-b161-5e7d0da650d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:12,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52093f74-b397-4877-b161-5e7d0da650d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:12,009] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:12,009] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:12,010] [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
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	100.0	1991	1996	95	conclusive
Segetibacter aerophilus	strain=NBRC 106135	GCA_007991655.1	670293	670293	type	True	77.0149	244	1996	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.5958	59	1996	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	76.2917	81	1996	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.2379	95	1996	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	75.9495	64	1996	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	75.9185	69	1996	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	75.9124	61	1996	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.8555	62	1996	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.7692	71	1996	95	below_threshold
Hanamia caeni	strain=BO-59	GCA_003721595.1	2294116	2294116	type	True	75.612	80	1996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:12,016] [INFO] DFAST Taxonomy check result was written to GCF_000374045.1_ASM37404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:12,017] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:12,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:12,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52093f74-b397-4877-b161-5e7d0da650d1/dqc_reference/checkm_data
[2024-01-24 13:10:12,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:12,080] [INFO] Task started: CheckM
[2024-01-24 13:10:12,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374045.1_ASM37404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374045.1_ASM37404v1_genomic.fna/checkm_input GCF_000374045.1_ASM37404v1_genomic.fna/checkm_result
[2024-01-24 13:11:16,409] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:16,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:16,433] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:16,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:16,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374045.1_ASM37404v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:16,435] [INFO] Task started: Blastn
[2024-01-24 13:11:16,435] [INFO] Running command: blastn -query GCF_000374045.1_ASM37404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52093f74-b397-4877-b161-5e7d0da650d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374045.1_ASM37404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:17,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:17,233] [INFO] Selected 25 target genomes.
[2024-01-24 13:11:17,234] [INFO] Target genome list was writen to GCF_000374045.1_ASM37404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:17,273] [INFO] Task started: fastANI
[2024-01-24 13:11:17,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed338a0-cb1d-4e51-889a-57b68594c624/GCF_000374045.1_ASM37404v1_genomic.fna.gz --refList GCF_000374045.1_ASM37404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374045.1_ASM37404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:33,321] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:33,339] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:33,340] [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_000374045.1	s__Segetibacter koreensis	100.0	1992	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007991655.1	s__Segetibacter aerophilus	77.0255	243	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355875.1	s__Segetibacter sp017355875	76.4087	109	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050375.1	s__Segetibacter sp002050375	76.4073	160	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Segetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971225.1	s__Panacibacter ginsenosidivorans	76.2565	94	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019130065.1	s__Parasegetibacter sp019130065	75.9739	63	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parasegetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013106755.1	s__Panacibacter sp013106755	75.8071	69	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881425.1	s__CAILAF01 sp903881425	75.6321	64	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.80	99.80	0.95	0.95	2	-
GCF_003721595.1	s__Ginsengibacter sp003721595	75.6275	79	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963365.1	s__AWTP1-9 sp003963365	75.5628	77	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266775.1	s__Ferruginibacter sp018266775	75.5351	50	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267725.1	s__CW01 sp018267725	75.5003	82	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	97.77	97.12	0.93	0.90	5	-
GCA_903832075.1	s__CAILAF01 sp903832075	75.4956	53	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247895.1	s__Parafilimonas sp019247895	75.3432	60	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642275.1	s__Parafilimonas sp903642275	75.2642	74	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268035.1	s__Parafilimonas sp018268035	75.1169	75	1996	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:33,341] [INFO] GTDB search result was written to GCF_000374045.1_ASM37404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:33,342] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:33,346] [INFO] DFAST_QC result json was written to GCF_000374045.1_ASM37404v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:33,346] [INFO] DFAST_QC completed!
[2024-01-24 13:11:33,347] [INFO] Total running time: 0h2m5s