[2024-01-24 11:19:53,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:53,852] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:53,852] [INFO] DQC Reference Directory: /var/lib/cwl/stg56f579a2-3bdd-4e75-8154-e85eb46b6822/dqc_reference
[2024-01-24 11:19:55,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,277] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,277] [INFO] Running command: gunzip -c /var/lib/cwl/stgeed8d233-802b-45f7-ae68-37e1473f0694/GCF_007989005.1_ASM798900v1_genomic.fna.gz | prodigal -d GCF_007989005.1_ASM798900v1_genomic.fna/cds.fna -a GCF_007989005.1_ASM798900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:09,310] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:09,311] [INFO] Task started: HMMsearch
[2024-01-24 11:20:09,311] [INFO] Running command: hmmsearch --tblout GCF_007989005.1_ASM798900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56f579a2-3bdd-4e75-8154-e85eb46b6822/dqc_reference/reference_markers.hmm GCF_007989005.1_ASM798900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:09,597] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:09,598] [INFO] Found 6/6 markers.
[2024-01-24 11:20:09,630] [INFO] Query marker FASTA was written to GCF_007989005.1_ASM798900v1_genomic.fna/markers.fasta
[2024-01-24 11:20:09,631] [INFO] Task started: Blastn
[2024-01-24 11:20:09,631] [INFO] Running command: blastn -query GCF_007989005.1_ASM798900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56f579a2-3bdd-4e75-8154-e85eb46b6822/dqc_reference/reference_markers.fasta -out GCF_007989005.1_ASM798900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:10,406] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:10,410] [INFO] Selected 13 target genomes.
[2024-01-24 11:20:10,411] [INFO] Target genome list was writen to GCF_007989005.1_ASM798900v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:10,417] [INFO] Task started: fastANI
[2024-01-24 11:20:10,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgeed8d233-802b-45f7-ae68-37e1473f0694/GCF_007989005.1_ASM798900v1_genomic.fna.gz --refList GCF_007989005.1_ASM798900v1_genomic.fna/target_genomes.txt --output GCF_007989005.1_ASM798900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:22,397] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:22,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56f579a2-3bdd-4e75-8154-e85eb46b6822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:22,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56f579a2-3bdd-4e75-8154-e85eb46b6822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:22,412] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:20:22,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:22,412] [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 glycines	strain=NBRC 105008	GCA_007989005.1	551990	551990	type	True	100.0	1305	1305	95	conclusive
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	99.9987	1302	1305	95	conclusive
Flavobacterium glycines	strain=NBRC 105008	GCA_001686935.1	551990	551990	type	True	99.9928	1301	1305	95	conclusive
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	86.9604	983	1305	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	83.9933	904	1305	95	below_threshold
Flavobacterium commune	strain=PK15	GCA_001857965.1	1306519	1306519	type	True	83.9853	936	1305	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	83.6505	890	1305	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	82.7203	819	1305	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	79.0442	421	1305	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	79.0122	402	1305	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.7681	401	1305	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.6246	455	1305	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.0067	150	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:22,414] [INFO] DFAST Taxonomy check result was written to GCF_007989005.1_ASM798900v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:22,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:22,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:22,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56f579a2-3bdd-4e75-8154-e85eb46b6822/dqc_reference/checkm_data
[2024-01-24 11:20:22,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:22,460] [INFO] Task started: CheckM
[2024-01-24 11:20:22,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989005.1_ASM798900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989005.1_ASM798900v1_genomic.fna/checkm_input GCF_007989005.1_ASM798900v1_genomic.fna/checkm_result
[2024-01-24 11:21:05,550] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:05,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:05,572] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:05,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:05,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989005.1_ASM798900v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:05,573] [INFO] Task started: Blastn
[2024-01-24 11:21:05,573] [INFO] Running command: blastn -query GCF_007989005.1_ASM798900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56f579a2-3bdd-4e75-8154-e85eb46b6822/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989005.1_ASM798900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:06,574] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:06,578] [INFO] Selected 9 target genomes.
[2024-01-24 11:21:06,578] [INFO] Target genome list was writen to GCF_007989005.1_ASM798900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:06,607] [INFO] Task started: fastANI
[2024-01-24 11:21:06,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgeed8d233-802b-45f7-ae68-37e1473f0694/GCF_007989005.1_ASM798900v1_genomic.fna.gz --refList GCF_007989005.1_ASM798900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989005.1_ASM798900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:15,132] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:15,142] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:15,143] [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_900100165.1	s__Flavobacterium glycines	99.9987	1302	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_014639535.1	s__Flavobacterium palustre	86.98	981	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016525.1	s__Flavobacterium sufflavum	84.4309	957	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001857965.1	s__Flavobacterium commune	83.9948	935	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.64	97.64	0.89	0.89	2	-
GCF_000425425.1	s__Flavobacterium daejeonense	83.9787	905	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	83.7578	876	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596575.1	s__Flavobacterium pokkalii	83.6889	886	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.93	96.93	0.85	0.85	2	-
GCA_002454195.1	s__Flavobacterium sp002454195	83.0112	560	1305	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695795.1	s__Flavobacterium seoulense	82.7177	819	1305	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 11:21:15,144] [INFO] GTDB search result was written to GCF_007989005.1_ASM798900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:15,145] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:15,148] [INFO] DFAST_QC result json was written to GCF_007989005.1_ASM798900v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:15,148] [INFO] DFAST_QC completed!
[2024-01-24 11:21:15,148] [INFO] Total running time: 0h1m21s