[2024-01-24 11:30:49,517] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d2bc547-3e7a-4cf7-8427-22749958a52f/dqc_reference
[2024-01-24 11:30:50,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,700] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,700] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c3e4c1e-2f49-4d7e-a67f-e93c25768141/GCF_003663835.1_ASM366383v1_genomic.fna.gz | prodigal -d GCF_003663835.1_ASM366383v1_genomic.fna/cds.fna -a GCF_003663835.1_ASM366383v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:05,805] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:05,806] [INFO] Task started: HMMsearch
[2024-01-24 11:31:05,806] [INFO] Running command: hmmsearch --tblout GCF_003663835.1_ASM366383v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d2bc547-3e7a-4cf7-8427-22749958a52f/dqc_reference/reference_markers.hmm GCF_003663835.1_ASM366383v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:06,067] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:06,068] [INFO] Found 6/6 markers.
[2024-01-24 11:31:06,097] [INFO] Query marker FASTA was written to GCF_003663835.1_ASM366383v1_genomic.fna/markers.fasta
[2024-01-24 11:31:06,098] [INFO] Task started: Blastn
[2024-01-24 11:31:06,098] [INFO] Running command: blastn -query GCF_003663835.1_ASM366383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d2bc547-3e7a-4cf7-8427-22749958a52f/dqc_reference/reference_markers.fasta -out GCF_003663835.1_ASM366383v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:06,772] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:06,776] [INFO] Selected 11 target genomes.
[2024-01-24 11:31:06,776] [INFO] Target genome list was writen to GCF_003663835.1_ASM366383v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:06,784] [INFO] Task started: fastANI
[2024-01-24 11:31:06,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c3e4c1e-2f49-4d7e-a67f-e93c25768141/GCF_003663835.1_ASM366383v1_genomic.fna.gz --refList GCF_003663835.1_ASM366383v1_genomic.fna/target_genomes.txt --output GCF_003663835.1_ASM366383v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:14,692] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:14,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d2bc547-3e7a-4cf7-8427-22749958a52f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:14,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d2bc547-3e7a-4cf7-8427-22749958a52f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:14,704] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:31:14,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:14,704] [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
Flavobacterium lindanitolerans	strain=DSM 21886	GCA_003663835.1	428988	428988	type	True	100.0	1231	1231	95	conclusive
Flavobacterium lindanitolerans	strain=IP-10	GCA_002846575.1	428988	428988	type	True	99.999	1231	1231	95	conclusive
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	87.2032	1063	1231	95	below_threshold
Flavobacterium gossypii	strain=DSM 100397	GCA_014138495.1	1646119	1646119	type	True	81.67	813	1231	95	below_threshold
Flavobacterium endophyticum	strain=DSM 29537	GCA_003634455.1	1540163	1540163	type	True	81.6004	827	1231	95	below_threshold
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	78.0835	272	1231	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.63	194	1231	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.149	99	1231	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.9686	103	1231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:14,706] [INFO] DFAST Taxonomy check result was written to GCF_003663835.1_ASM366383v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:14,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:14,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:14,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d2bc547-3e7a-4cf7-8427-22749958a52f/dqc_reference/checkm_data
[2024-01-24 11:31:14,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:14,743] [INFO] Task started: CheckM
[2024-01-24 11:31:14,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003663835.1_ASM366383v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003663835.1_ASM366383v1_genomic.fna/checkm_input GCF_003663835.1_ASM366383v1_genomic.fna/checkm_result
[2024-01-24 11:32:00,690] [INFO] Task succeeded: CheckM
[2024-01-24 11:32:00,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:32:00,709] [INFO] ===== Completeness check finished =====
[2024-01-24 11:32:00,710] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:32:00,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003663835.1_ASM366383v1_genomic.fna/markers.fasta)
[2024-01-24 11:32:00,711] [INFO] Task started: Blastn
[2024-01-24 11:32:00,711] [INFO] Running command: blastn -query GCF_003663835.1_ASM366383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d2bc547-3e7a-4cf7-8427-22749958a52f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003663835.1_ASM366383v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:32:01,618] [INFO] Task succeeded: Blastn
[2024-01-24 11:32:01,622] [INFO] Selected 12 target genomes.
[2024-01-24 11:32:01,623] [INFO] Target genome list was writen to GCF_003663835.1_ASM366383v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:32:01,632] [INFO] Task started: fastANI
[2024-01-24 11:32:01,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c3e4c1e-2f49-4d7e-a67f-e93c25768141/GCF_003663835.1_ASM366383v1_genomic.fna.gz --refList GCF_003663835.1_ASM366383v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003663835.1_ASM366383v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:10,048] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:10,064] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:10,064] [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_002846575.1	s__Flavobacterium lindanitolerans	99.999	1231	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	conclusive
GCF_006385255.1	s__Flavobacterium microcysteis	87.2032	1063	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634455.1	s__Flavobacterium endophyticum	81.5995	827	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.19	97.19	0.95	0.95	2	-
GCF_003865365.1	s__Flavobacterium macacae	79.1749	414	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422705.1	s__Flavobacterium soli	78.0835	272	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711165.2	s__Flavobacterium sp009711165	77.7982	192	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425465.1	s__Flavobacterium filum	77.6901	150	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482975.1	s__Flavobacterium sp002482975	77.5152	190	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638005.1	s__Flavobacterium orientale	77.4506	165	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752255.1	s__Flavobacterium sp015752255	77.236	182	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634195.1	s__Flavobacterium sp004634195	77.217	109	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.56	97.13	0.95	0.91	3	-
GCA_002428305.1	s__Flavobacterium sp002428305	76.8708	165	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:32:10,066] [INFO] GTDB search result was written to GCF_003663835.1_ASM366383v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:10,066] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:10,070] [INFO] DFAST_QC result json was written to GCF_003663835.1_ASM366383v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:10,070] [INFO] DFAST_QC completed!
[2024-01-24 11:32:10,070] [INFO] Total running time: 0h1m21s