[2024-01-25 18:37:05,451] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:05,453] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:05,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg69d7de6f-01dc-4d79-8c2d-b4ce1927b53f/dqc_reference
[2024-01-25 18:37:06,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:06,575] [INFO] Task started: Prodigal
[2024-01-25 18:37:06,576] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2e97f0e-97a7-4263-b403-77a16a48947a/GCF_002302565.1_ASM230256v1_genomic.fna.gz | prodigal -d GCF_002302565.1_ASM230256v1_genomic.fna/cds.fna -a GCF_002302565.1_ASM230256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:15,110] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:15,111] [INFO] Task started: HMMsearch
[2024-01-25 18:37:15,111] [INFO] Running command: hmmsearch --tblout GCF_002302565.1_ASM230256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69d7de6f-01dc-4d79-8c2d-b4ce1927b53f/dqc_reference/reference_markers.hmm GCF_002302565.1_ASM230256v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:15,306] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:15,307] [INFO] Found 6/6 markers.
[2024-01-25 18:37:15,328] [INFO] Query marker FASTA was written to GCF_002302565.1_ASM230256v1_genomic.fna/markers.fasta
[2024-01-25 18:37:15,329] [INFO] Task started: Blastn
[2024-01-25 18:37:15,329] [INFO] Running command: blastn -query GCF_002302565.1_ASM230256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69d7de6f-01dc-4d79-8c2d-b4ce1927b53f/dqc_reference/reference_markers.fasta -out GCF_002302565.1_ASM230256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:15,891] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:15,894] [INFO] Selected 13 target genomes.
[2024-01-25 18:37:15,894] [INFO] Target genome list was writen to GCF_002302565.1_ASM230256v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:15,962] [INFO] Task started: fastANI
[2024-01-25 18:37:15,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e97f0e-97a7-4263-b403-77a16a48947a/GCF_002302565.1_ASM230256v1_genomic.fna.gz --refList GCF_002302565.1_ASM230256v1_genomic.fna/target_genomes.txt --output GCF_002302565.1_ASM230256v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:37:23,326] [INFO] Task succeeded: fastANI
[2024-01-25 18:37:23,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69d7de6f-01dc-4d79-8c2d-b4ce1927b53f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:37:23,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69d7de6f-01dc-4d79-8c2d-b4ce1927b53f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:37:23,332] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:37:23,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:37:23,333] [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
Capnocytophaga canimorsus	strain=7120	GCA_002302565.1	28188	28188	type	True	100.0	799	804	95	conclusive
Capnocytophaga canimorsus	strain=NCTC12242	GCA_900460905.1	28188	28188	type	True	99.9988	802	804	95	conclusive
Capnocytophaga canimorsus	strain=DSM 19204	GCA_002797785.1	28188	28188	type	True	99.9797	778	804	95	conclusive
Capnocytophaga cynodegmi	strain=E6447	GCA_000379185.1	28189	28189	type	True	87.925	307	804	95	below_threshold
Capnocytophaga canis	strain=CcD38	GCA_000827555.1	1848903	1848903	type	True	86.0067	220	804	95	below_threshold
Capnocytophaga felis	strain=KC07070	GCA_009684755.1	2267611	2267611	type	True	80.6185	289	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:37:23,334] [INFO] DFAST Taxonomy check result was written to GCF_002302565.1_ASM230256v1_genomic.fna/tc_result.tsv
[2024-01-25 18:37:23,334] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:37:23,334] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:37:23,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69d7de6f-01dc-4d79-8c2d-b4ce1927b53f/dqc_reference/checkm_data
[2024-01-25 18:37:23,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:37:23,361] [INFO] Task started: CheckM
[2024-01-25 18:37:23,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002302565.1_ASM230256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002302565.1_ASM230256v1_genomic.fna/checkm_input GCF_002302565.1_ASM230256v1_genomic.fna/checkm_result
[2024-01-25 18:37:52,035] [INFO] Task succeeded: CheckM
[2024-01-25 18:37:52,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:37:52,064] [INFO] ===== Completeness check finished =====
[2024-01-25 18:37:52,064] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:37:52,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002302565.1_ASM230256v1_genomic.fna/markers.fasta)
[2024-01-25 18:37:52,064] [INFO] Task started: Blastn
[2024-01-25 18:37:52,064] [INFO] Running command: blastn -query GCF_002302565.1_ASM230256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69d7de6f-01dc-4d79-8c2d-b4ce1927b53f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002302565.1_ASM230256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:52,927] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:52,931] [INFO] Selected 20 target genomes.
[2024-01-25 18:37:52,931] [INFO] Target genome list was writen to GCF_002302565.1_ASM230256v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:37:52,959] [INFO] Task started: fastANI
[2024-01-25 18:37:52,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e97f0e-97a7-4263-b403-77a16a48947a/GCF_002302565.1_ASM230256v1_genomic.fna.gz --refList GCF_002302565.1_ASM230256v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002302565.1_ASM230256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:38:04,087] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:04,093] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:38:04,094] [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_002302565.1	s__Capnocytophaga canimorsus	100.0	802	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	98.20	97.29	0.93	0.87	15	conclusive
GCF_000379185.1	s__Capnocytophaga cynodegmi	87.8818	308	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.53	96.05	0.91	0.86	7	-
GCF_000827555.1	s__Capnocytophaga canis	86.0067	220	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	98.20	97.91	0.92	0.88	11	-
GCF_002302635.1	s__Capnocytophaga stomatis	81.7021	311	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	97.71	97.65	0.92	0.91	4	-
GCF_009684755.1	s__Capnocytophaga felis	80.5681	291	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000023285.1	s__Capnocytophaga ochracea	78.2227	68	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Capnocytophaga	95.0	96.34	96.09	0.90	0.87	17	-
GCF_013389595.1	s__Flavobacterium sp013389595	77.3257	54	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352465.1	s__Kordia sp003352465	76.6273	58	804	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:38:04,095] [INFO] GTDB search result was written to GCF_002302565.1_ASM230256v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:38:04,096] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:38:04,098] [INFO] DFAST_QC result json was written to GCF_002302565.1_ASM230256v1_genomic.fna/dqc_result.json
[2024-01-25 18:38:04,098] [INFO] DFAST_QC completed!
[2024-01-25 18:38:04,098] [INFO] Total running time: 0h0m59s