[2024-01-24 13:27:46,057] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,058] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e493bea-01ec-4481-ae66-30041da4c143/dqc_reference
[2024-01-24 13:27:47,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,460] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,461] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fbee54a-aa44-49bc-946e-448f765cd87a/GCF_014638465.1_ASM1463846v1_genomic.fna.gz | prodigal -d GCF_014638465.1_ASM1463846v1_genomic.fna/cds.fna -a GCF_014638465.1_ASM1463846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:57,055] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:57,055] [INFO] Task started: HMMsearch
[2024-01-24 13:27:57,055] [INFO] Running command: hmmsearch --tblout GCF_014638465.1_ASM1463846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e493bea-01ec-4481-ae66-30041da4c143/dqc_reference/reference_markers.hmm GCF_014638465.1_ASM1463846v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:57,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:57,361] [INFO] Found 6/6 markers.
[2024-01-24 13:27:57,391] [INFO] Query marker FASTA was written to GCF_014638465.1_ASM1463846v1_genomic.fna/markers.fasta
[2024-01-24 13:27:57,392] [INFO] Task started: Blastn
[2024-01-24 13:27:57,392] [INFO] Running command: blastn -query GCF_014638465.1_ASM1463846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e493bea-01ec-4481-ae66-30041da4c143/dqc_reference/reference_markers.fasta -out GCF_014638465.1_ASM1463846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:58,041] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:58,044] [INFO] Selected 10 target genomes.
[2024-01-24 13:27:58,044] [INFO] Target genome list was writen to GCF_014638465.1_ASM1463846v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:58,065] [INFO] Task started: fastANI
[2024-01-24 13:27:58,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fbee54a-aa44-49bc-946e-448f765cd87a/GCF_014638465.1_ASM1463846v1_genomic.fna.gz --refList GCF_014638465.1_ASM1463846v1_genomic.fna/target_genomes.txt --output GCF_014638465.1_ASM1463846v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:04,976] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:04,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e493bea-01ec-4481-ae66-30041da4c143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:04,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e493bea-01ec-4481-ae66-30041da4c143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:04,993] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:04,993] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:04,993] [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
Chishuiella changwenlii	strain=CGMCC 1.12707	GCA_014638465.1	1434701	1434701	type	True	100.0	1115	1118	95	conclusive
Chishuiella changwenlii	strain=DSM 27989	GCA_900142565.1	1434701	1434701	type	True	99.9877	1115	1118	95	conclusive
Empedobacter tilapiae	strain=MRS2	GCA_004785645.1	2491114	2491114	type	True	81.145	608	1118	95	below_threshold
Empedobacter brevis	strain=ATCC 43319	GCA_000382425.1	247	247	type	True	80.8459	569	1118	95	below_threshold
Empedobacter brevis	strain=NBRC 14943	GCA_007990795.1	247	247	type	True	80.7578	577	1118	95	below_threshold
Faecalibacter macacae	strain=YIM 102668	GCA_003687725.1	1859289	1859289	type	True	79.6074	430	1118	95	below_threshold
Faecalibacter bovis	strain=ZY171143	GCA_017948305.1	2898187	2898187	type	True	79.3322	425	1118	95	below_threshold
Faecalibacter rhinopitheci	strain=WQ 117	GCA_015234135.1	2779678	2779678	type	True	79.1311	405	1118	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	75.7187	86	1118	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.3179	104	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:04,994] [INFO] DFAST Taxonomy check result was written to GCF_014638465.1_ASM1463846v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:04,995] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:04,995] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:04,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e493bea-01ec-4481-ae66-30041da4c143/dqc_reference/checkm_data
[2024-01-24 13:28:04,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:05,032] [INFO] Task started: CheckM
[2024-01-24 13:28:05,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638465.1_ASM1463846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638465.1_ASM1463846v1_genomic.fna/checkm_input GCF_014638465.1_ASM1463846v1_genomic.fna/checkm_result
[2024-01-24 13:28:38,138] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:38,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:38,158] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:38,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:38,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638465.1_ASM1463846v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:38,159] [INFO] Task started: Blastn
[2024-01-24 13:28:38,159] [INFO] Running command: blastn -query GCF_014638465.1_ASM1463846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e493bea-01ec-4481-ae66-30041da4c143/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638465.1_ASM1463846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:39,040] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:39,043] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:39,043] [INFO] Target genome list was writen to GCF_014638465.1_ASM1463846v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:39,065] [INFO] Task started: fastANI
[2024-01-24 13:28:39,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fbee54a-aa44-49bc-946e-448f765cd87a/GCF_014638465.1_ASM1463846v1_genomic.fna.gz --refList GCF_014638465.1_ASM1463846v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638465.1_ASM1463846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:46,320] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:46,329] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:46,329] [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_900142565.1	s__Chishuiella changwenlii	99.9877	1115	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_002430925.1	s__Chishuiella sp002430925	81.5856	555	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378465.1	s__Empedobacter sp002378465	81.3719	603	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.64	95.90	0.90	0.86	24	-
GCA_002484335.1	s__Chishuiella sp002484335	81.3215	619	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013488205.1	s__Empedobacter falsenii_A	81.2951	639	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.19	95.74	0.91	0.86	9	-
GCF_013116755.1	s__Empedobacter stercoris	81.2412	529	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	99.07	99.07	0.96	0.96	2	-
GCF_004785645.1	s__Empedobacter tilapiae	81.1445	606	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115015.1	s__Algoriella xinjiangensis	81.1302	615	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Algoriella	95.0	98.62	97.69	0.94	0.93	3	-
GCF_000382425.1	s__Empedobacter brevis	80.8459	569	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	98.11	96.51	0.89	0.85	7	-
GCA_003687725.1	s__Faecalibacter macacae	79.6324	429	1118	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Faecalibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:46,331] [INFO] GTDB search result was written to GCF_014638465.1_ASM1463846v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:46,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:46,334] [INFO] DFAST_QC result json was written to GCF_014638465.1_ASM1463846v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:46,334] [INFO] DFAST_QC completed!
[2024-01-24 13:28:46,334] [INFO] Total running time: 0h1m0s