[2024-01-25 18:37:35,514] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:37:35,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:37:35,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgedeb4073-c19b-4fcf-8d98-651f032706a3/dqc_reference
[2024-01-25 18:37:36,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:37:36,675] [INFO] Task started: Prodigal
[2024-01-25 18:37:36,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg077ce30a-324a-41a7-8b90-0fb978c28a9d/GCF_002920895.1_ASM292089v1_genomic.fna.gz | prodigal -d GCF_002920895.1_ASM292089v1_genomic.fna/cds.fna -a GCF_002920895.1_ASM292089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:37:50,095] [INFO] Task succeeded: Prodigal
[2024-01-25 18:37:50,095] [INFO] Task started: HMMsearch
[2024-01-25 18:37:50,095] [INFO] Running command: hmmsearch --tblout GCF_002920895.1_ASM292089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedeb4073-c19b-4fcf-8d98-651f032706a3/dqc_reference/reference_markers.hmm GCF_002920895.1_ASM292089v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:37:50,363] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:37:50,367] [INFO] Found 6/6 markers.
[2024-01-25 18:37:50,397] [INFO] Query marker FASTA was written to GCF_002920895.1_ASM292089v1_genomic.fna/markers.fasta
[2024-01-25 18:37:50,397] [INFO] Task started: Blastn
[2024-01-25 18:37:50,397] [INFO] Running command: blastn -query GCF_002920895.1_ASM292089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedeb4073-c19b-4fcf-8d98-651f032706a3/dqc_reference/reference_markers.fasta -out GCF_002920895.1_ASM292089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:37:51,044] [INFO] Task succeeded: Blastn
[2024-01-25 18:37:51,047] [INFO] Selected 17 target genomes.
[2024-01-25 18:37:51,048] [INFO] Target genome list was writen to GCF_002920895.1_ASM292089v1_genomic.fna/target_genomes.txt
[2024-01-25 18:37:51,054] [INFO] Task started: fastANI
[2024-01-25 18:37:51,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg077ce30a-324a-41a7-8b90-0fb978c28a9d/GCF_002920895.1_ASM292089v1_genomic.fna.gz --refList GCF_002920895.1_ASM292089v1_genomic.fna/target_genomes.txt --output GCF_002920895.1_ASM292089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:38:05,291] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:05,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedeb4073-c19b-4fcf-8d98-651f032706a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:38:05,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedeb4073-c19b-4fcf-8d98-651f032706a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:38:05,303] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:38:05,303] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:38:05,303] [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 alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	100.0	1262	1263	95	conclusive
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	83.0953	768	1263	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	82.1524	773	1263	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	81.8648	707	1263	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	79.6962	612	1263	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.4294	451	1263	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	79.1344	415	1263	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	79.1149	419	1263	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.0385	455	1263	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	78.1807	418	1263	95	below_threshold
Flavobacterium hibernum	strain=DSM 12611	GCA_000832125.1	37752	37752	type	True	78.1719	411	1263	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.1348	355	1263	95	below_threshold
Flavobacterium hibernum	strain=NCTC13514	GCA_900450525.1	37752	37752	type	True	78.125	412	1263	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.1058	370	1263	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.1058	370	1263	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.0968	359	1263	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.3248	201	1263	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:38:05,305] [INFO] DFAST Taxonomy check result was written to GCF_002920895.1_ASM292089v1_genomic.fna/tc_result.tsv
[2024-01-25 18:38:05,305] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:38:05,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:38:05,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedeb4073-c19b-4fcf-8d98-651f032706a3/dqc_reference/checkm_data
[2024-01-25 18:38:05,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:38:05,351] [INFO] Task started: CheckM
[2024-01-25 18:38:05,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002920895.1_ASM292089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002920895.1_ASM292089v1_genomic.fna/checkm_input GCF_002920895.1_ASM292089v1_genomic.fna/checkm_result
[2024-01-25 18:38:45,918] [INFO] Task succeeded: CheckM
[2024-01-25 18:38:45,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:38:45,935] [INFO] ===== Completeness check finished =====
[2024-01-25 18:38:45,935] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:38:45,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002920895.1_ASM292089v1_genomic.fna/markers.fasta)
[2024-01-25 18:38:45,936] [INFO] Task started: Blastn
[2024-01-25 18:38:45,936] [INFO] Running command: blastn -query GCF_002920895.1_ASM292089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedeb4073-c19b-4fcf-8d98-651f032706a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002920895.1_ASM292089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:38:46,880] [INFO] Task succeeded: Blastn
[2024-01-25 18:38:46,882] [INFO] Selected 12 target genomes.
[2024-01-25 18:38:46,883] [INFO] Target genome list was writen to GCF_002920895.1_ASM292089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:38:46,895] [INFO] Task started: fastANI
[2024-01-25 18:38:46,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg077ce30a-324a-41a7-8b90-0fb978c28a9d/GCF_002920895.1_ASM292089v1_genomic.fna.gz --refList GCF_002920895.1_ASM292089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002920895.1_ASM292089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:38:56,850] [INFO] Task succeeded: fastANI
[2024-01-25 18:38:56,858] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:38:56,859] [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_002920895.1	s__Flavobacterium alvei	100.0	1262	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007097365.1	s__Flavobacterium franklandianum	83.1206	766	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_014379405.1	s__Flavobacterium sp014379405	82.3737	659	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129545.1	s__Flavobacterium fluvii	82.1657	772	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355225.1	s__Flavobacterium nackdongense	81.8542	707	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823965.1	s__Flavobacterium sp013823965	81.7313	627	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003449615.1	s__Flavobacterium sp003449615	81.5746	486	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277675.1	s__Flavobacterium soyangense	81.3472	595	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989775.1	s__Flavobacterium sp017989775	81.2655	368	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.62	98.46	0.76	0.72	3	-
GCF_002813295.1	s__Flavobacterium sp002813295	79.1569	453	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754195.1	s__Flavobacterium sp002754195	78.3048	402	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832125.1	s__Flavobacterium hibernum	78.1681	412	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:38:56,861] [INFO] GTDB search result was written to GCF_002920895.1_ASM292089v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:38:56,862] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:38:56,865] [INFO] DFAST_QC result json was written to GCF_002920895.1_ASM292089v1_genomic.fna/dqc_result.json
[2024-01-25 18:38:56,865] [INFO] DFAST_QC completed!
[2024-01-25 18:38:56,865] [INFO] Total running time: 0h1m21s