[2024-01-25 20:14:50,300] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,302] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg1674d47b-cef5-4481-a51a-c71b051b6ae2/dqc_reference
[2024-01-25 20:14:51,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:51,524] [INFO] Task started: Prodigal
[2024-01-25 20:14:51,524] [INFO] Running command: gunzip -c /var/lib/cwl/stgc455639e-8ceb-4c62-92b2-d17ac32481fd/GCF_900186945.1_48903_E01_genomic.fna.gz | prodigal -d GCF_900186945.1_48903_E01_genomic.fna/cds.fna -a GCF_900186945.1_48903_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:57,716] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:57,716] [INFO] Task started: HMMsearch
[2024-01-25 20:14:57,716] [INFO] Running command: hmmsearch --tblout GCF_900186945.1_48903_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1674d47b-cef5-4481-a51a-c71b051b6ae2/dqc_reference/reference_markers.hmm GCF_900186945.1_48903_E01_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:57,908] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:57,909] [INFO] Found 6/6 markers.
[2024-01-25 20:14:57,932] [INFO] Query marker FASTA was written to GCF_900186945.1_48903_E01_genomic.fna/markers.fasta
[2024-01-25 20:14:57,933] [INFO] Task started: Blastn
[2024-01-25 20:14:57,933] [INFO] Running command: blastn -query GCF_900186945.1_48903_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1674d47b-cef5-4481-a51a-c71b051b6ae2/dqc_reference/reference_markers.fasta -out GCF_900186945.1_48903_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:58,502] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:58,505] [INFO] Selected 13 target genomes.
[2024-01-25 20:14:58,506] [INFO] Target genome list was writen to GCF_900186945.1_48903_E01_genomic.fna/target_genomes.txt
[2024-01-25 20:14:58,512] [INFO] Task started: fastANI
[2024-01-25 20:14:58,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgc455639e-8ceb-4c62-92b2-d17ac32481fd/GCF_900186945.1_48903_E01_genomic.fna.gz --refList GCF_900186945.1_48903_E01_genomic.fna/target_genomes.txt --output GCF_900186945.1_48903_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:06,166] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:06,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1674d47b-cef5-4481-a51a-c71b051b6ae2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:06,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1674d47b-cef5-4481-a51a-c71b051b6ae2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:06,175] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:15:06,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:06,175] [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
Riemerella anatipestifer	strain=NCTC11014	GCA_900186945.1	34085	34085	type	True	100.0	717	718	95	conclusive
Riemerella anatipestifer	strain=DSM 15868	GCA_000183155.1	34085	34085	type	True	99.9956	718	718	95	conclusive
Riemerella anatipestifer	strain=ATCC 11845	GCA_000252855.1	34085	34085	type	True	99.9943	716	718	95	conclusive
Chryseobacterium phocaeense	strain=6021061333	GCA_900169075.1	1816690	1816690	type	True	78.4168	69	718	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	78.2676	74	718	95	below_threshold
Chryseobacterium taklimakanense	strain=NCTC13490	GCA_900187185.1	536441	536441	type	True	78.1874	61	718	95	below_threshold
Riemerella columbina	strain=DSM 16469	GCA_000374405.1	103810	103810	type	True	78.1058	204	718	95	below_threshold
Elizabethkingia miricola	strain=DSM 14571	GCA_008124555.1	172045	172045	type	True	77.8235	68	718	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	77.6583	78	718	95	below_threshold
Riemerella columbipharyngis	strain=DSM 24015	GCA_900101995.1	1071918	1071918	type	True	77.5513	118	718	95	below_threshold
Elizabethkingia occulta	strain=G4070	GCA_002023715.1	1867263	1867263	type	True	77.4628	74	718	95	below_threshold
Cloacibacterium rupense	strain=CGMCC 1.7656	GCA_014645495.1	517423	517423	type	True	77.4139	114	718	95	below_threshold
Chryseobacterium taihuense	strain=CGMCC 1.10941	GCA_900103755.1	1141221	1141221	type	True	76.9021	74	718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:06,177] [INFO] DFAST Taxonomy check result was written to GCF_900186945.1_48903_E01_genomic.fna/tc_result.tsv
[2024-01-25 20:15:06,177] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:06,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:06,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1674d47b-cef5-4481-a51a-c71b051b6ae2/dqc_reference/checkm_data
[2024-01-25 20:15:06,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:06,205] [INFO] Task started: CheckM
[2024-01-25 20:15:06,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900186945.1_48903_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900186945.1_48903_E01_genomic.fna/checkm_input GCF_900186945.1_48903_E01_genomic.fna/checkm_result
[2024-01-25 20:15:28,233] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:28,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:28,251] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:28,251] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:28,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900186945.1_48903_E01_genomic.fna/markers.fasta)
[2024-01-25 20:15:28,251] [INFO] Task started: Blastn
[2024-01-25 20:15:28,251] [INFO] Running command: blastn -query GCF_900186945.1_48903_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1674d47b-cef5-4481-a51a-c71b051b6ae2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900186945.1_48903_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:29,016] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:29,019] [INFO] Selected 13 target genomes.
[2024-01-25 20:15:29,019] [INFO] Target genome list was writen to GCF_900186945.1_48903_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:29,080] [INFO] Task started: fastANI
[2024-01-25 20:15:29,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgc455639e-8ceb-4c62-92b2-d17ac32481fd/GCF_900186945.1_48903_E01_genomic.fna.gz --refList GCF_900186945.1_48903_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900186945.1_48903_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:35,746] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:35,755] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:35,755] [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_000252855.1	s__Riemerella anatipestifer	99.9943	716	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Riemerella	95.0	97.90	95.12	0.93	0.81	76	conclusive
GCF_009670965.1	s__Riemerella anatipestifer_B	94.3825	579	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Riemerella	95.0	95.18	95.18	0.86	0.86	2	-
GCF_009663465.1	s__Riemerella anatipestifer_C	93.9143	588	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Riemerella	95.0	96.04	95.95	0.82	0.80	3	-
GCF_000374405.1	s__Riemerella columbina	78.1228	203	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Riemerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614945.1	s__Bergeyella_A cardium	77.8861	66	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Bergeyella_A	95.0	98.84	98.84	0.96	0.96	2	-
GCF_001675285.1	s__Elizabethkingia miricola	77.7779	69	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Elizabethkingia	95.0	97.66	96.19	0.91	0.86	23	-
GCA_013333255.2	s__JABCPE02 sp013333255	77.7159	85	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__JABCPE02	95.0	96.35	96.35	0.93	0.93	2	-
GCF_902728305.1	s__Chryseobacterium sp902728305	77.5808	87	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900101995.1	s__Riemerella columbipharyngis	77.5764	117	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Riemerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645495.1	s__Cloacibacterium rupense	77.4151	114	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799515.1	s__Chryseobacterium sp000799515	77.0426	86	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103755.1	s__Chryseobacterium taihuense	76.9784	74	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.40	97.39	0.91	0.91	3	-
GCA_002337005.1	s__Cloacibacterium sp002337005	76.4294	123	718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Cloacibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:35,756] [INFO] GTDB search result was written to GCF_900186945.1_48903_E01_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:35,757] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:35,759] [INFO] DFAST_QC result json was written to GCF_900186945.1_48903_E01_genomic.fna/dqc_result.json
[2024-01-25 20:15:35,759] [INFO] DFAST_QC completed!
[2024-01-25 20:15:35,759] [INFO] Total running time: 0h0m45s