[2023-06-29 09:02:17,141] [INFO] DFAST_QC pipeline started.
[2023-06-29 09:02:17,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 09:02:17,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg41343eee-c312-44e9-9c82-c5753fbbe169/dqc_reference
[2023-06-29 09:02:18,466] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 09:02:18,467] [INFO] Task started: Prodigal
[2023-06-29 09:02:18,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ba688a1-9c53-4f8c-96db-d615d47a24d6/GCA_020048955.1_ASM2004895v1_genomic.fna.gz | prodigal -d GCA_020048955.1_ASM2004895v1_genomic.fna/cds.fna -a GCA_020048955.1_ASM2004895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 09:02:27,734] [INFO] Task succeeded: Prodigal
[2023-06-29 09:02:27,734] [INFO] Task started: HMMsearch
[2023-06-29 09:02:27,734] [INFO] Running command: hmmsearch --tblout GCA_020048955.1_ASM2004895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41343eee-c312-44e9-9c82-c5753fbbe169/dqc_reference/reference_markers.hmm GCA_020048955.1_ASM2004895v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 09:02:28,016] [INFO] Task succeeded: HMMsearch
[2023-06-29 09:02:28,017] [INFO] Found 6/6 markers.
[2023-06-29 09:02:28,053] [INFO] Query marker FASTA was written to GCA_020048955.1_ASM2004895v1_genomic.fna/markers.fasta
[2023-06-29 09:02:28,054] [INFO] Task started: Blastn
[2023-06-29 09:02:28,054] [INFO] Running command: blastn -query GCA_020048955.1_ASM2004895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41343eee-c312-44e9-9c82-c5753fbbe169/dqc_reference/reference_markers.fasta -out GCA_020048955.1_ASM2004895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:02:28,760] [INFO] Task succeeded: Blastn
[2023-06-29 09:02:28,765] [INFO] Selected 16 target genomes.
[2023-06-29 09:02:28,766] [INFO] Target genome list was writen to GCA_020048955.1_ASM2004895v1_genomic.fna/target_genomes.txt
[2023-06-29 09:02:28,772] [INFO] Task started: fastANI
[2023-06-29 09:02:28,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ba688a1-9c53-4f8c-96db-d615d47a24d6/GCA_020048955.1_ASM2004895v1_genomic.fna.gz --refList GCA_020048955.1_ASM2004895v1_genomic.fna/target_genomes.txt --output GCA_020048955.1_ASM2004895v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 09:02:38,801] [INFO] Task succeeded: fastANI
[2023-06-29 09:02:38,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41343eee-c312-44e9-9c82-c5753fbbe169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 09:02:38,802] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41343eee-c312-44e9-9c82-c5753fbbe169/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 09:02:38,814] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 09:02:38,814] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 09:02:38,815] [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 aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	82.0042	483	866	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	81.9739	486	866	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	81.9107	474	866	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	79.4659	380	866	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	79.3802	378	866	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	79.3475	383	866	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	79.2691	365	866	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	78.5052	296	866	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.0267	234	866	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.8071	250	866	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.6077	244	866	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.5301	234	866	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.127	207	866	95	below_threshold
Flavobacterium succinicans	strain=DSM 4002	GCA_900114945.1	29536	29536	type	True	77.1174	183	866	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.0168	220	866	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	76.8168	213	866	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 09:02:38,817] [INFO] DFAST Taxonomy check result was written to GCA_020048955.1_ASM2004895v1_genomic.fna/tc_result.tsv
[2023-06-29 09:02:38,817] [INFO] ===== Taxonomy check completed =====
[2023-06-29 09:02:38,817] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 09:02:38,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41343eee-c312-44e9-9c82-c5753fbbe169/dqc_reference/checkm_data
[2023-06-29 09:02:38,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 09:02:38,858] [INFO] Task started: CheckM
[2023-06-29 09:02:38,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020048955.1_ASM2004895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020048955.1_ASM2004895v1_genomic.fna/checkm_input GCA_020048955.1_ASM2004895v1_genomic.fna/checkm_result
[2023-06-29 09:03:11,422] [INFO] Task succeeded: CheckM
[2023-06-29 09:03:11,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.18%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 09:03:11,447] [INFO] ===== Completeness check finished =====
[2023-06-29 09:03:11,448] [INFO] ===== Start GTDB Search =====
[2023-06-29 09:03:11,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020048955.1_ASM2004895v1_genomic.fna/markers.fasta)
[2023-06-29 09:03:11,448] [INFO] Task started: Blastn
[2023-06-29 09:03:11,449] [INFO] Running command: blastn -query GCA_020048955.1_ASM2004895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41343eee-c312-44e9-9c82-c5753fbbe169/dqc_reference/reference_markers_gtdb.fasta -out GCA_020048955.1_ASM2004895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 09:03:12,441] [INFO] Task succeeded: Blastn
[2023-06-29 09:03:12,446] [INFO] Selected 11 target genomes.
[2023-06-29 09:03:12,446] [INFO] Target genome list was writen to GCA_020048955.1_ASM2004895v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 09:03:12,452] [INFO] Task started: fastANI
[2023-06-29 09:03:12,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ba688a1-9c53-4f8c-96db-d615d47a24d6/GCA_020048955.1_ASM2004895v1_genomic.fna.gz --refList GCA_020048955.1_ASM2004895v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020048955.1_ASM2004895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 09:03:19,749] [INFO] Task succeeded: fastANI
[2023-06-29 09:03:19,762] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 09:03:19,763] [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_013298525.1	s__Flavobacterium sp013298525	88.5385	541	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	88.532	640	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	81.9618	487	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCA_003525665.1	s__Flavobacterium sp003525665	81.8514	482	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879645.1	s__Flavobacterium sp903879645	79.7667	313	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913315.1	s__Flavobacterium sp903913315	79.7357	342	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.66	99.66	0.86	0.86	2	-
GCF_004362665.1	s__Flavobacterium dankookense	79.4531	381	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888655.1	s__Flavobacterium sp903888655	79.4184	286	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911605.1	s__Flavobacterium sp012911605	79.2814	364	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902795.1	s__Flavobacterium sp903902795	77.982	276	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032075.1	s__Flavobacterium sp012032075	76.8735	192	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 09:03:19,765] [INFO] GTDB search result was written to GCA_020048955.1_ASM2004895v1_genomic.fna/result_gtdb.tsv
[2023-06-29 09:03:19,765] [INFO] ===== GTDB Search completed =====
[2023-06-29 09:03:19,769] [INFO] DFAST_QC result json was written to GCA_020048955.1_ASM2004895v1_genomic.fna/dqc_result.json
[2023-06-29 09:03:19,769] [INFO] DFAST_QC completed!
[2023-06-29 09:03:19,769] [INFO] Total running time: 0h1m3s