[2024-01-24 14:06:30,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgce5699d9-6899-4325-aedb-68c4d53a0cef/dqc_reference
[2024-01-24 14:06:31,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,698] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a3722f1-d4c6-48f3-80ce-88c04fd94331/GCF_006491595.2_ASM649159v2_genomic.fna.gz | prodigal -d GCF_006491595.2_ASM649159v2_genomic.fna/cds.fna -a GCF_006491595.2_ASM649159v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:46,006] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:46,006] [INFO] Task started: HMMsearch
[2024-01-24 14:06:46,006] [INFO] Running command: hmmsearch --tblout GCF_006491595.2_ASM649159v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce5699d9-6899-4325-aedb-68c4d53a0cef/dqc_reference/reference_markers.hmm GCF_006491595.2_ASM649159v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:46,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:46,319] [INFO] Found 6/6 markers.
[2024-01-24 14:06:46,363] [INFO] Query marker FASTA was written to GCF_006491595.2_ASM649159v2_genomic.fna/markers.fasta
[2024-01-24 14:06:46,363] [INFO] Task started: Blastn
[2024-01-24 14:06:46,363] [INFO] Running command: blastn -query GCF_006491595.2_ASM649159v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgce5699d9-6899-4325-aedb-68c4d53a0cef/dqc_reference/reference_markers.fasta -out GCF_006491595.2_ASM649159v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:47,170] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:47,174] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:47,175] [INFO] Target genome list was writen to GCF_006491595.2_ASM649159v2_genomic.fna/target_genomes.txt
[2024-01-24 14:06:47,233] [INFO] Task started: fastANI
[2024-01-24 14:06:47,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a3722f1-d4c6-48f3-80ce-88c04fd94331/GCF_006491595.2_ASM649159v2_genomic.fna.gz --refList GCF_006491595.2_ASM649159v2_genomic.fna/target_genomes.txt --output GCF_006491595.2_ASM649159v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:56,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:56,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce5699d9-6899-4325-aedb-68c4d53a0cef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:56,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce5699d9-6899-4325-aedb-68c4d53a0cef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:56,387] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:56,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:56,387] [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 jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	100.0	1554	1556	95	conclusive
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	81.0801	827	1556	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	81.0747	828	1556	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	80.9194	741	1556	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	80.5381	759	1556	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	78.7405	408	1556	95	below_threshold
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	78.6553	415	1556	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.5305	348	1556	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.4664	386	1556	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.2633	386	1556	95	below_threshold
Flavobacterium bernardetii	strain=F-372	GCA_011305415.1	2813823	2813823	type	True	77.6091	326	1556	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.1041	239	1556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:56,389] [INFO] DFAST Taxonomy check result was written to GCF_006491595.2_ASM649159v2_genomic.fna/tc_result.tsv
[2024-01-24 14:06:56,389] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:56,389] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:56,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce5699d9-6899-4325-aedb-68c4d53a0cef/dqc_reference/checkm_data
[2024-01-24 14:06:56,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:56,435] [INFO] Task started: CheckM
[2024-01-24 14:06:56,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006491595.2_ASM649159v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006491595.2_ASM649159v2_genomic.fna/checkm_input GCF_006491595.2_ASM649159v2_genomic.fna/checkm_result
[2024-01-24 14:07:41,558] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:41,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:41,581] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:41,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:41,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006491595.2_ASM649159v2_genomic.fna/markers.fasta)
[2024-01-24 14:07:41,583] [INFO] Task started: Blastn
[2024-01-24 14:07:41,583] [INFO] Running command: blastn -query GCF_006491595.2_ASM649159v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgce5699d9-6899-4325-aedb-68c4d53a0cef/dqc_reference/reference_markers_gtdb.fasta -out GCF_006491595.2_ASM649159v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:42,708] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:42,711] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:42,711] [INFO] Target genome list was writen to GCF_006491595.2_ASM649159v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:42,721] [INFO] Task started: fastANI
[2024-01-24 14:07:42,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a3722f1-d4c6-48f3-80ce-88c04fd94331/GCF_006491595.2_ASM649159v2_genomic.fna.gz --refList GCF_006491595.2_ASM649159v2_genomic.fna/target_genomes_gtdb.txt --output GCF_006491595.2_ASM649159v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:50,622] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:50,636] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:50,636] [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_006491595.2	s__Flavobacterium jejuense	100.0	1554	1556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012032075.1	s__Flavobacterium sp012032075	81.4285	580	1556	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	81.0956	825	1556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004303025.1	s__Flavobacterium sp004303025	80.9135	858	1556	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	80.8503	777	1556	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	80.834	780	1556	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	80.825	757	1556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506265.1	s__Flavobacterium sp902506265	80.6915	790	1556	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 14:07:50,638] [INFO] GTDB search result was written to GCF_006491595.2_ASM649159v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:50,639] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:50,642] [INFO] DFAST_QC result json was written to GCF_006491595.2_ASM649159v2_genomic.fna/dqc_result.json
[2024-01-24 14:07:50,643] [INFO] DFAST_QC completed!
[2024-01-24 14:07:50,643] [INFO] Total running time: 0h1m20s