[2024-01-25 18:58:35,630] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:35,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:35,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bff79c0-85c1-4855-9b4a-3b6abd2b83df/dqc_reference
[2024-01-25 18:58:36,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:36,761] [INFO] Task started: Prodigal
[2024-01-25 18:58:36,761] [INFO] Running command: gunzip -c /var/lib/cwl/stg984d09d7-dd4e-41d0-ac24-f6046626469c/GCF_009711525.1_ASM971152v1_genomic.fna.gz | prodigal -d GCF_009711525.1_ASM971152v1_genomic.fna/cds.fna -a GCF_009711525.1_ASM971152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:51,126] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:51,126] [INFO] Task started: HMMsearch
[2024-01-25 18:58:51,126] [INFO] Running command: hmmsearch --tblout GCF_009711525.1_ASM971152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bff79c0-85c1-4855-9b4a-3b6abd2b83df/dqc_reference/reference_markers.hmm GCF_009711525.1_ASM971152v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:51,469] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:51,470] [INFO] Found 6/6 markers.
[2024-01-25 18:58:51,511] [INFO] Query marker FASTA was written to GCF_009711525.1_ASM971152v1_genomic.fna/markers.fasta
[2024-01-25 18:58:51,512] [INFO] Task started: Blastn
[2024-01-25 18:58:51,512] [INFO] Running command: blastn -query GCF_009711525.1_ASM971152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bff79c0-85c1-4855-9b4a-3b6abd2b83df/dqc_reference/reference_markers.fasta -out GCF_009711525.1_ASM971152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:52,083] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:52,086] [INFO] Selected 23 target genomes.
[2024-01-25 18:58:52,086] [INFO] Target genome list was writen to GCF_009711525.1_ASM971152v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:52,109] [INFO] Task started: fastANI
[2024-01-25 18:58:52,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg984d09d7-dd4e-41d0-ac24-f6046626469c/GCF_009711525.1_ASM971152v1_genomic.fna.gz --refList GCF_009711525.1_ASM971152v1_genomic.fna/target_genomes.txt --output GCF_009711525.1_ASM971152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:13,683] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:13,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bff79c0-85c1-4855-9b4a-3b6abd2b83df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:13,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bff79c0-85c1-4855-9b4a-3b6abd2b83df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:13,690] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:59:13,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:13,690] [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
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	100.0	1400	1419	95	conclusive
Fulvivirga lutea	strain=S481	GCA_017068455.1	2810512	2810512	type	True	77.4137	178	1419	95	below_threshold
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	76.9011	84	1419	95	below_threshold
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	76.8043	92	1419	95	below_threshold
Fulvivirga aurantia	strain=RKSG066	GCA_009711475.1	2529383	2529383	type	True	76.7177	71	1419	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	76.5224	84	1419	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:13,692] [INFO] DFAST Taxonomy check result was written to GCF_009711525.1_ASM971152v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:13,693] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:13,693] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:13,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bff79c0-85c1-4855-9b4a-3b6abd2b83df/dqc_reference/checkm_data
[2024-01-25 18:59:13,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:13,741] [INFO] Task started: CheckM
[2024-01-25 18:59:13,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711525.1_ASM971152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711525.1_ASM971152v1_genomic.fna/checkm_input GCF_009711525.1_ASM971152v1_genomic.fna/checkm_result
[2024-01-25 18:59:57,553] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:57,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:57,575] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:57,575] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:57,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711525.1_ASM971152v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:57,576] [INFO] Task started: Blastn
[2024-01-25 18:59:57,576] [INFO] Running command: blastn -query GCF_009711525.1_ASM971152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bff79c0-85c1-4855-9b4a-3b6abd2b83df/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711525.1_ASM971152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:58,338] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:58,341] [INFO] Selected 26 target genomes.
[2024-01-25 18:59:58,341] [INFO] Target genome list was writen to GCF_009711525.1_ASM971152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:58,363] [INFO] Task started: fastANI
[2024-01-25 18:59:58,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg984d09d7-dd4e-41d0-ac24-f6046626469c/GCF_009711525.1_ASM971152v1_genomic.fna.gz --refList GCF_009711525.1_ASM971152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711525.1_ASM971152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:20,628] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:20,634] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:20,635] [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_009711525.1	s__Fulvivirga lutimaris	100.0	1400	1419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017068455.1	s__Fulvivirga sp017068455	77.3968	179	1419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338655.1	s__Fulvivirga sp002338655	77.1035	180	1419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757215.1	s__Fulvivirga sp016757215	76.8043	92	1419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711475.1	s__Fulvivirga aurantia	76.7177	71	1419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331535.1	s__Fulvivirga imtechensis	76.5224	84	1419	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:20,636] [INFO] GTDB search result was written to GCF_009711525.1_ASM971152v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:20,636] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:20,640] [INFO] DFAST_QC result json was written to GCF_009711525.1_ASM971152v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:20,640] [INFO] DFAST_QC completed!
[2024-01-25 19:00:20,640] [INFO] Total running time: 0h1m45s