[2024-01-24 15:27:20,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:20,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:20,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg4145441f-9e6f-4a19-a199-fad8a93dc7bc/dqc_reference
[2024-01-24 15:27:23,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,291] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d46e053-e7fc-4add-8e4d-dd0539c86ab2/GCF_014644395.1_ASM1464439v1_genomic.fna.gz | prodigal -d GCF_014644395.1_ASM1464439v1_genomic.fna/cds.fna -a GCF_014644395.1_ASM1464439v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:41,685] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:41,685] [INFO] Task started: HMMsearch
[2024-01-24 15:27:41,685] [INFO] Running command: hmmsearch --tblout GCF_014644395.1_ASM1464439v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4145441f-9e6f-4a19-a199-fad8a93dc7bc/dqc_reference/reference_markers.hmm GCF_014644395.1_ASM1464439v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:41,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:41,993] [INFO] Found 6/6 markers.
[2024-01-24 15:27:42,042] [INFO] Query marker FASTA was written to GCF_014644395.1_ASM1464439v1_genomic.fna/markers.fasta
[2024-01-24 15:27:42,042] [INFO] Task started: Blastn
[2024-01-24 15:27:42,043] [INFO] Running command: blastn -query GCF_014644395.1_ASM1464439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4145441f-9e6f-4a19-a199-fad8a93dc7bc/dqc_reference/reference_markers.fasta -out GCF_014644395.1_ASM1464439v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:42,734] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:42,738] [INFO] Selected 13 target genomes.
[2024-01-24 15:27:42,739] [INFO] Target genome list was writen to GCF_014644395.1_ASM1464439v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:42,750] [INFO] Task started: fastANI
[2024-01-24 15:27:42,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d46e053-e7fc-4add-8e4d-dd0539c86ab2/GCF_014644395.1_ASM1464439v1_genomic.fna.gz --refList GCF_014644395.1_ASM1464439v1_genomic.fna/target_genomes.txt --output GCF_014644395.1_ASM1464439v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:58,606] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:58,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4145441f-9e6f-4a19-a199-fad8a93dc7bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:58,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4145441f-9e6f-4a19-a199-fad8a93dc7bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:58,630] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:58,630] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:58,631] [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 limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	100.0	1783	1785	95	conclusive
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	99.996	1772	1785	95	conclusive
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	86.9181	1251	1785	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	86.7746	1353	1785	95	below_threshold
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	86.4415	1167	1785	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	84.7761	1255	1785	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	81.8255	882	1785	95	below_threshold
Flavobacterium resistens	strain=DSM 19382	GCA_009674815.1	443612	443612	type	True	81.8141	890	1785	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.7236	927	1785	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.5617	885	1785	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.4819	920	1785	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.3046	883	1785	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.3594	195	1785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:58,632] [INFO] DFAST Taxonomy check result was written to GCF_014644395.1_ASM1464439v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:58,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:58,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:58,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4145441f-9e6f-4a19-a199-fad8a93dc7bc/dqc_reference/checkm_data
[2024-01-24 15:27:58,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:58,690] [INFO] Task started: CheckM
[2024-01-24 15:27:58,690] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644395.1_ASM1464439v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644395.1_ASM1464439v1_genomic.fna/checkm_input GCF_014644395.1_ASM1464439v1_genomic.fna/checkm_result
[2024-01-24 15:28:53,722] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:53,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:53,745] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:53,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:53,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644395.1_ASM1464439v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:53,746] [INFO] Task started: Blastn
[2024-01-24 15:28:53,746] [INFO] Running command: blastn -query GCF_014644395.1_ASM1464439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4145441f-9e6f-4a19-a199-fad8a93dc7bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644395.1_ASM1464439v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:54,772] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:54,777] [INFO] Selected 14 target genomes.
[2024-01-24 15:28:54,777] [INFO] Target genome list was writen to GCF_014644395.1_ASM1464439v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:54,788] [INFO] Task started: fastANI
[2024-01-24 15:28:54,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d46e053-e7fc-4add-8e4d-dd0539c86ab2/GCF_014644395.1_ASM1464439v1_genomic.fna.gz --refList GCF_014644395.1_ASM1464439v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644395.1_ASM1464439v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:12,211] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:12,235] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:12,236] [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_010645075.1	s__Flavobacterium limi	99.996	1772	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003202405.1	s__Flavobacterium hydrophilum	86.7655	1354	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645065.1	s__Flavobacterium fluviatile	86.4521	1166	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735715.2	s__Flavobacterium chungangense	85.0661	1290	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_010614725.1	s__Flavobacterium ajazii	84.7031	1236	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202435.1	s__Flavobacterium cheongpyeongense	84.4643	1178	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182645.1	s__Flavobacterium resistens	81.8291	890	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	81.8279	882	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745775.1	s__Flavobacterium sp000745775	81.8096	910	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833855.1	s__Flavobacterium sp017833855	81.8042	934	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688345.1	s__Flavobacterium sp003688345	81.7119	957	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142715.1	s__Flavobacterium pectinovorum	81.614	1000	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.60	0.94	0.89	3	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	81.511	942	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_000425445.1	s__Flavobacterium denitrificans	81.4757	864	1785	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 15:29:12,239] [INFO] GTDB search result was written to GCF_014644395.1_ASM1464439v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:12,240] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:12,246] [INFO] DFAST_QC result json was written to GCF_014644395.1_ASM1464439v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:12,247] [INFO] DFAST_QC completed!
[2024-01-24 15:29:12,247] [INFO] Total running time: 0h1m51s