[2024-01-25 19:50:20,462] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:20,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:20,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg8baf58aa-0fd1-4848-8cba-f728aed6b03e/dqc_reference
[2024-01-25 19:50:21,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:21,656] [INFO] Task started: Prodigal
[2024-01-25 19:50:21,656] [INFO] Running command: gunzip -c /var/lib/cwl/stg319d2e79-1684-4d6e-a30f-ac3bfeacf250/GCF_021650975.2_ASM2165097v2_genomic.fna.gz | prodigal -d GCF_021650975.2_ASM2165097v2_genomic.fna/cds.fna -a GCF_021650975.2_ASM2165097v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:33,528] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:33,529] [INFO] Task started: HMMsearch
[2024-01-25 19:50:33,529] [INFO] Running command: hmmsearch --tblout GCF_021650975.2_ASM2165097v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8baf58aa-0fd1-4848-8cba-f728aed6b03e/dqc_reference/reference_markers.hmm GCF_021650975.2_ASM2165097v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:33,840] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:33,841] [INFO] Found 6/6 markers.
[2024-01-25 19:50:33,887] [INFO] Query marker FASTA was written to GCF_021650975.2_ASM2165097v2_genomic.fna/markers.fasta
[2024-01-25 19:50:33,888] [INFO] Task started: Blastn
[2024-01-25 19:50:33,888] [INFO] Running command: blastn -query GCF_021650975.2_ASM2165097v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8baf58aa-0fd1-4848-8cba-f728aed6b03e/dqc_reference/reference_markers.fasta -out GCF_021650975.2_ASM2165097v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:34,568] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:34,573] [INFO] Selected 12 target genomes.
[2024-01-25 19:50:34,573] [INFO] Target genome list was writen to GCF_021650975.2_ASM2165097v2_genomic.fna/target_genomes.txt
[2024-01-25 19:50:34,585] [INFO] Task started: fastANI
[2024-01-25 19:50:34,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg319d2e79-1684-4d6e-a30f-ac3bfeacf250/GCF_021650975.2_ASM2165097v2_genomic.fna.gz --refList GCF_021650975.2_ASM2165097v2_genomic.fna/target_genomes.txt --output GCF_021650975.2_ASM2165097v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:43,866] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:43,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8baf58aa-0fd1-4848-8cba-f728aed6b03e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:43,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8baf58aa-0fd1-4848-8cba-f728aed6b03e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:43,877] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:50:43,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:43,877] [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 jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	100.0	1555	1560	95	conclusive
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	81.5242	816	1560	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	80.5601	757	1560	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.8731	575	1560	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.8695	574	1560	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.6413	374	1560	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.4771	373	1560	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	78.3073	376	1560	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	78.2404	305	1560	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.1842	352	1560	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	76.8006	221	1560	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.7084	104	1560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:43,879] [INFO] DFAST Taxonomy check result was written to GCF_021650975.2_ASM2165097v2_genomic.fna/tc_result.tsv
[2024-01-25 19:50:43,880] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:43,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:43,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8baf58aa-0fd1-4848-8cba-f728aed6b03e/dqc_reference/checkm_data
[2024-01-25 19:50:43,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:43,925] [INFO] Task started: CheckM
[2024-01-25 19:50:43,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021650975.2_ASM2165097v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021650975.2_ASM2165097v2_genomic.fna/checkm_input GCF_021650975.2_ASM2165097v2_genomic.fna/checkm_result
[2024-01-25 19:51:20,571] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:20,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:20,594] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:20,595] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:20,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021650975.2_ASM2165097v2_genomic.fna/markers.fasta)
[2024-01-25 19:51:20,595] [INFO] Task started: Blastn
[2024-01-25 19:51:20,595] [INFO] Running command: blastn -query GCF_021650975.2_ASM2165097v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8baf58aa-0fd1-4848-8cba-f728aed6b03e/dqc_reference/reference_markers_gtdb.fasta -out GCF_021650975.2_ASM2165097v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:21,571] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:21,574] [INFO] Selected 12 target genomes.
[2024-01-25 19:51:21,574] [INFO] Target genome list was writen to GCF_021650975.2_ASM2165097v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:21,600] [INFO] Task started: fastANI
[2024-01-25 19:51:21,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg319d2e79-1684-4d6e-a30f-ac3bfeacf250/GCF_021650975.2_ASM2165097v2_genomic.fna.gz --refList GCF_021650975.2_ASM2165097v2_genomic.fna/target_genomes_gtdb.txt --output GCF_021650975.2_ASM2165097v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:30,325] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:30,334] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:51:30,334] [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_000967805.1	s__Flavobacterium sp000967805	81.7337	825	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	80.5727	755	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032075.1	s__Flavobacterium sp012032075	79.26	478	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004303025.1	s__Flavobacterium sp004303025	79.0675	589	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862805.1	s__Flavobacterium sp002862805	79.0533	419	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	78.8923	573	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902506265.1	s__Flavobacterium sp902506265	78.8221	607	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715085.1	s__Flavobacterium sp002715085	78.7563	548	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862755.1	s__Flavobacterium sp002862755	78.6507	549	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	78.1924	350	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421645.1	s__Flavobacterium sp002421645	78.085	183	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352205.1	s__Flavobacterium sp002352205	76.9169	212	1560	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:30,335] [INFO] GTDB search result was written to GCF_021650975.2_ASM2165097v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:30,336] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:30,338] [INFO] DFAST_QC result json was written to GCF_021650975.2_ASM2165097v2_genomic.fna/dqc_result.json
[2024-01-25 19:51:30,339] [INFO] DFAST_QC completed!
[2024-01-25 19:51:30,339] [INFO] Total running time: 0h1m10s