[2024-01-24 10:57:11,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:11,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:11,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg94af11e4-6409-47b7-b9e5-31ada5696110/dqc_reference
[2024-01-24 10:57:13,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:13,206] [INFO] Task started: Prodigal
[2024-01-24 10:57:13,206] [INFO] Running command: gunzip -c /var/lib/cwl/stgda82d67a-f110-4576-bd13-f594b81c8845/GCF_019565455.1_ASM1956545v1_genomic.fna.gz | prodigal -d GCF_019565455.1_ASM1956545v1_genomic.fna/cds.fna -a GCF_019565455.1_ASM1956545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:22,692] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:22,692] [INFO] Task started: HMMsearch
[2024-01-24 10:57:22,692] [INFO] Running command: hmmsearch --tblout GCF_019565455.1_ASM1956545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94af11e4-6409-47b7-b9e5-31ada5696110/dqc_reference/reference_markers.hmm GCF_019565455.1_ASM1956545v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:23,013] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:23,014] [INFO] Found 6/6 markers.
[2024-01-24 10:57:23,053] [INFO] Query marker FASTA was written to GCF_019565455.1_ASM1956545v1_genomic.fna/markers.fasta
[2024-01-24 10:57:23,053] [INFO] Task started: Blastn
[2024-01-24 10:57:23,054] [INFO] Running command: blastn -query GCF_019565455.1_ASM1956545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94af11e4-6409-47b7-b9e5-31ada5696110/dqc_reference/reference_markers.fasta -out GCF_019565455.1_ASM1956545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:23,739] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:23,744] [INFO] Selected 14 target genomes.
[2024-01-24 10:57:23,745] [INFO] Target genome list was writen to GCF_019565455.1_ASM1956545v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:23,750] [INFO] Task started: fastANI
[2024-01-24 10:57:23,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgda82d67a-f110-4576-bd13-f594b81c8845/GCF_019565455.1_ASM1956545v1_genomic.fna.gz --refList GCF_019565455.1_ASM1956545v1_genomic.fna/target_genomes.txt --output GCF_019565455.1_ASM1956545v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:34,028] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:34,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94af11e4-6409-47b7-b9e5-31ada5696110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:34,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94af11e4-6409-47b7-b9e5-31ada5696110/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:34,041] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:34,042] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:34,042] [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 oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	100.0	1179	1180	95	conclusive
Flavobacterium columnare	strain=NBRC 100251	GCA_007990835.1	996	996	type	True	84.0532	721	1180	95	below_threshold
Flavobacterium columnare	strain=ATCC 23463	GCA_002530675.1	996	996	type	True	83.9041	752	1180	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	83.7989	804	1180	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	78.593	321	1180	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	78.062	187	1180	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	77.9973	237	1180	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	77.7301	234	1180	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.6605	270	1180	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	77.4378	136	1180	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	77.3798	133	1180	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.0841	140	1180	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	77.0661	146	1180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:34,050] [INFO] DFAST Taxonomy check result was written to GCF_019565455.1_ASM1956545v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:34,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:34,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:34,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94af11e4-6409-47b7-b9e5-31ada5696110/dqc_reference/checkm_data
[2024-01-24 10:57:34,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:34,118] [INFO] Task started: CheckM
[2024-01-24 10:57:34,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019565455.1_ASM1956545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019565455.1_ASM1956545v1_genomic.fna/checkm_input GCF_019565455.1_ASM1956545v1_genomic.fna/checkm_result
[2024-01-24 10:58:06,853] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:06,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:06,869] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:06,869] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:06,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019565455.1_ASM1956545v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:06,870] [INFO] Task started: Blastn
[2024-01-24 10:58:06,870] [INFO] Running command: blastn -query GCF_019565455.1_ASM1956545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94af11e4-6409-47b7-b9e5-31ada5696110/dqc_reference/reference_markers_gtdb.fasta -out GCF_019565455.1_ASM1956545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:07,833] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:07,836] [INFO] Selected 9 target genomes.
[2024-01-24 10:58:07,837] [INFO] Target genome list was writen to GCF_019565455.1_ASM1956545v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:07,848] [INFO] Task started: fastANI
[2024-01-24 10:58:07,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgda82d67a-f110-4576-bd13-f594b81c8845/GCF_019565455.1_ASM1956545v1_genomic.fna.gz --refList GCF_019565455.1_ASM1956545v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019565455.1_ASM1956545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:14,496] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:14,504] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:14,504] [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_002204895.1	s__Flavobacterium columnare_C	99.0566	976	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.67	99.21	0.94	0.90	7	conclusive
GCF_002530675.1	s__Flavobacterium columnare	83.904	752	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.33	99.02	0.96	0.93	39	-
GCA_002217245.1	s__Flavobacterium columnare_A	83.7992	730	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.08	98.79	0.92	0.89	11	-
GCF_900290975.1	s__Flavobacterium columnare_D	83.7503	767	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.86	98.55	0.90	0.88	3	-
GCF_004959765.1	s__Flavobacterium sp004959765	78.7343	319	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142035.1	s__Flavobacterium terrae	78.6033	322	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122165.1	s__Flavobacterium sp004122165	77.9926	236	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	77.4393	277	1180	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	77.3748	134	1180	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 10:58:14,506] [INFO] GTDB search result was written to GCF_019565455.1_ASM1956545v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:14,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:14,510] [INFO] DFAST_QC result json was written to GCF_019565455.1_ASM1956545v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:14,511] [INFO] DFAST_QC completed!
[2024-01-24 10:58:14,511] [INFO] Total running time: 0h1m3s