[2024-01-24 11:42:20,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:42:20,309] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:42:20,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg74590ab7-2e06-42c2-9d2b-c2053b9be5de/dqc_reference
[2024-01-24 11:42:24,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:42:24,524] [INFO] Task started: Prodigal
[2024-01-24 11:42:24,524] [INFO] Running command: gunzip -c /var/lib/cwl/stg042e7a99-2318-400b-977c-61010a68a495/GCF_002355595.1_F._lacunae_YT21-2_genomic.fna.gz | prodigal -d GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/cds.fna -a GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:02,200] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:02,200] [INFO] Task started: HMMsearch
[2024-01-24 11:43:02,201] [INFO] Running command: hmmsearch --tblout GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74590ab7-2e06-42c2-9d2b-c2053b9be5de/dqc_reference/reference_markers.hmm GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:02,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:02,605] [INFO] Found 6/6 markers.
[2024-01-24 11:43:02,666] [INFO] Query marker FASTA was written to GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/markers.fasta
[2024-01-24 11:43:02,666] [INFO] Task started: Blastn
[2024-01-24 11:43:02,666] [INFO] Running command: blastn -query GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/markers.fasta -db /var/lib/cwl/stg74590ab7-2e06-42c2-9d2b-c2053b9be5de/dqc_reference/reference_markers.fasta -out GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:03,237] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:03,264] [INFO] Selected 11 target genomes.
[2024-01-24 11:43:03,265] [INFO] Target genome list was writen to GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/target_genomes.txt
[2024-01-24 11:43:03,271] [INFO] Task started: fastANI
[2024-01-24 11:43:03,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg042e7a99-2318-400b-977c-61010a68a495/GCF_002355595.1_F._lacunae_YT21-2_genomic.fna.gz --refList GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/target_genomes.txt --output GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:16,779] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:16,780] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74590ab7-2e06-42c2-9d2b-c2053b9be5de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:16,780] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74590ab7-2e06-42c2-9d2b-c2053b9be5de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:16,790] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:43:16,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:16,790] [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
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	100.0	2603	2604	95	conclusive
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	99.9933	2564	2604	95	conclusive
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	79.7404	929	2604	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	77.2699	287	2604	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	77.2523	293	2604	95	below_threshold
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	76.5741	68	2604	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	76.5043	148	2604	95	below_threshold
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	76.4243	88	2604	95	below_threshold
Flavihumibacter profundi	strain=KCTC 62290	GCA_020076305.1	2716883	2716883	type	True	76.3501	61	2604	95	below_threshold
Niabella yanshanensis	strain=HAMBI_3031	GCA_003349965.1	577386	577386	type	True	76.0322	75	2604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:16,792] [INFO] DFAST Taxonomy check result was written to GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/tc_result.tsv
[2024-01-24 11:43:16,792] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:16,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:16,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74590ab7-2e06-42c2-9d2b-c2053b9be5de/dqc_reference/checkm_data
[2024-01-24 11:43:16,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:16,865] [INFO] Task started: CheckM
[2024-01-24 11:43:16,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/checkm_input GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/checkm_result
[2024-01-24 11:44:54,085] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:54,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:54,108] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:54,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:54,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/markers.fasta)
[2024-01-24 11:44:54,110] [INFO] Task started: Blastn
[2024-01-24 11:44:54,110] [INFO] Running command: blastn -query GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/markers.fasta -db /var/lib/cwl/stg74590ab7-2e06-42c2-9d2b-c2053b9be5de/dqc_reference/reference_markers_gtdb.fasta -out GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:54,881] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:54,885] [INFO] Selected 10 target genomes.
[2024-01-24 11:44:54,885] [INFO] Target genome list was writen to GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:54,899] [INFO] Task started: fastANI
[2024-01-24 11:44:54,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg042e7a99-2318-400b-977c-61010a68a495/GCF_002355595.1_F._lacunae_YT21-2_genomic.fna.gz --refList GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/target_genomes_gtdb.txt --output GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:07,058] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:07,075] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:07,075] [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_002355595.1	s__Filimonas lacunae	100.0	2603	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003097095.1	s__Filimonas sp003097095	79.8953	1007	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641615.1	s__Filimonas zeae	79.7357	929	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994055.1	s__Filimonas endophytica	79.6664	851	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118675.1	s__Filimonas effusa	77.2652	289	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412455.1	s__Deminuibacter soli	77.2427	294	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Deminuibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	77.112	193	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744515.1	s__Paraflavitalea sp017744515	76.0422	98	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349965.1	s__Niabella yanshanensis	76.0322	75	2604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,077] [INFO] GTDB search result was written to GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:07,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:07,081] [INFO] DFAST_QC result json was written to GCF_002355595.1_F._lacunae_YT21-2_genomic.fna/dqc_result.json
[2024-01-24 11:45:07,082] [INFO] DFAST_QC completed!
[2024-01-24 11:45:07,082] [INFO] Total running time: 0h2m47s