[2024-01-24 13:41:20,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg03811c63-e197-446c-9c88-8c0362e514aa/dqc_reference
[2024-01-24 13:41:21,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,861] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,861] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa97ba11-f1ca-4d6e-905e-fe15982c7b05/GCF_027111315.2_ASM2711131v2_genomic.fna.gz | prodigal -d GCF_027111315.2_ASM2711131v2_genomic.fna/cds.fna -a GCF_027111315.2_ASM2711131v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:49,286] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:49,286] [INFO] Task started: HMMsearch
[2024-01-24 13:41:49,286] [INFO] Running command: hmmsearch --tblout GCF_027111315.2_ASM2711131v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03811c63-e197-446c-9c88-8c0362e514aa/dqc_reference/reference_markers.hmm GCF_027111315.2_ASM2711131v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:49,588] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:49,589] [INFO] Found 6/6 markers.
[2024-01-24 13:41:49,626] [INFO] Query marker FASTA was written to GCF_027111315.2_ASM2711131v2_genomic.fna/markers.fasta
[2024-01-24 13:41:49,627] [INFO] Task started: Blastn
[2024-01-24 13:41:49,627] [INFO] Running command: blastn -query GCF_027111315.2_ASM2711131v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg03811c63-e197-446c-9c88-8c0362e514aa/dqc_reference/reference_markers.fasta -out GCF_027111315.2_ASM2711131v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:50,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:50,405] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:50,406] [INFO] Target genome list was writen to GCF_027111315.2_ASM2711131v2_genomic.fna/target_genomes.txt
[2024-01-24 13:41:50,412] [INFO] Task started: fastANI
[2024-01-24 13:41:50,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa97ba11-f1ca-4d6e-905e-fe15982c7b05/GCF_027111315.2_ASM2711131v2_genomic.fna.gz --refList GCF_027111315.2_ASM2711131v2_genomic.fna/target_genomes.txt --output GCF_027111315.2_ASM2711131v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:05,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:05,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03811c63-e197-446c-9c88-8c0362e514aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:05,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03811c63-e197-446c-9c88-8c0362e514aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:05,879] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:42:05,879] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:42:05,879] [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 fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	86.1087	961	1503	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	82.638	740	1503	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	82.2985	830	1503	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	81.188	690	1503	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	79.9099	639	1503	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.1437	511	1503	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	79.0966	414	1503	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	79.0406	390	1503	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	78.9834	449	1503	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	78.8487	427	1503	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.5536	325	1503	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_002222055.1	946678	946678	type	True	78.5339	324	1503	95	below_threshold
Flavobacterium araucananum	strain=DSM 24704	GCA_003148525.1	946678	946678	type	True	78.4568	331	1503	95	below_threshold
Flavobacterium succinicans	strain=DSM 4002	GCA_900114945.1	29536	29536	type	True	78.2353	334	1503	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.9686	329	1503	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.915	347	1503	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.6284	162	1503	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.0285	145	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:05,881] [INFO] DFAST Taxonomy check result was written to GCF_027111315.2_ASM2711131v2_genomic.fna/tc_result.tsv
[2024-01-24 13:42:05,882] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:05,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:05,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03811c63-e197-446c-9c88-8c0362e514aa/dqc_reference/checkm_data
[2024-01-24 13:42:05,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:05,936] [INFO] Task started: CheckM
[2024-01-24 13:42:05,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027111315.2_ASM2711131v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027111315.2_ASM2711131v2_genomic.fna/checkm_input GCF_027111315.2_ASM2711131v2_genomic.fna/checkm_result
[2024-01-24 13:43:19,279] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:19,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:19,302] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:19,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:19,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027111315.2_ASM2711131v2_genomic.fna/markers.fasta)
[2024-01-24 13:43:19,303] [INFO] Task started: Blastn
[2024-01-24 13:43:19,303] [INFO] Running command: blastn -query GCF_027111315.2_ASM2711131v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg03811c63-e197-446c-9c88-8c0362e514aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_027111315.2_ASM2711131v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:20,195] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:20,201] [INFO] Selected 13 target genomes.
[2024-01-24 13:43:20,201] [INFO] Target genome list was writen to GCF_027111315.2_ASM2711131v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:20,228] [INFO] Task started: fastANI
[2024-01-24 13:43:20,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa97ba11-f1ca-4d6e-905e-fe15982c7b05/GCF_027111315.2_ASM2711131v2_genomic.fna.gz --refList GCF_027111315.2_ASM2711131v2_genomic.fna/target_genomes_gtdb.txt --output GCF_027111315.2_ASM2711131v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:30,326] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:30,343] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:43:30,343] [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
GCA_017989775.1	s__Flavobacterium sp017989775	86.4855	442	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.62	98.46	0.76	0.72	3	-
GCF_900129545.1	s__Flavobacterium fluvii	86.1164	960	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379405.1	s__Flavobacterium sp014379405	85.7345	829	1503	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	83.985	717	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	82.6254	741	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCF_002920895.1	s__Flavobacterium alvei	82.2983	831	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365135.1	s__Flavobacterium sp010365135	81.6143	585	1503	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	81.4016	622	1503	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	81.1693	694	1503	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	80.9193	448	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861155.1	s__Flavobacterium sp903861155	80.6631	503	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCF_002797935.1	s__Flavobacterium sp002797935	79.4796	515	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222055.1	s__Flavobacterium araucananum	78.4963	327	1503	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:30,345] [INFO] GTDB search result was written to GCF_027111315.2_ASM2711131v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:30,345] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:30,351] [INFO] DFAST_QC result json was written to GCF_027111315.2_ASM2711131v2_genomic.fna/dqc_result.json
[2024-01-24 13:43:30,351] [INFO] DFAST_QC completed!
[2024-01-24 13:43:30,351] [INFO] Total running time: 0h2m10s