[2024-01-25 19:45:20,879] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:20,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:20,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e3f28b0-2d55-431f-a268-4d782eea3eba/dqc_reference
[2024-01-25 19:45:22,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:22,082] [INFO] Task started: Prodigal
[2024-01-25 19:45:22,082] [INFO] Running command: gunzip -c /var/lib/cwl/stgc52b35d4-c2b3-4825-a941-21edc6583517/GCF_018595675.2_ASM1859567v2_genomic.fna.gz | prodigal -d GCF_018595675.2_ASM1859567v2_genomic.fna/cds.fna -a GCF_018595675.2_ASM1859567v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:43,588] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:43,588] [INFO] Task started: HMMsearch
[2024-01-25 19:45:43,588] [INFO] Running command: hmmsearch --tblout GCF_018595675.2_ASM1859567v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e3f28b0-2d55-431f-a268-4d782eea3eba/dqc_reference/reference_markers.hmm GCF_018595675.2_ASM1859567v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:43,857] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:43,858] [INFO] Found 6/6 markers.
[2024-01-25 19:45:43,905] [INFO] Query marker FASTA was written to GCF_018595675.2_ASM1859567v2_genomic.fna/markers.fasta
[2024-01-25 19:45:43,905] [INFO] Task started: Blastn
[2024-01-25 19:45:43,905] [INFO] Running command: blastn -query GCF_018595675.2_ASM1859567v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3f28b0-2d55-431f-a268-4d782eea3eba/dqc_reference/reference_markers.fasta -out GCF_018595675.2_ASM1859567v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:44,443] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:44,445] [INFO] Selected 17 target genomes.
[2024-01-25 19:45:44,446] [INFO] Target genome list was writen to GCF_018595675.2_ASM1859567v2_genomic.fna/target_genomes.txt
[2024-01-25 19:45:44,472] [INFO] Task started: fastANI
[2024-01-25 19:45:44,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52b35d4-c2b3-4825-a941-21edc6583517/GCF_018595675.2_ASM1859567v2_genomic.fna.gz --refList GCF_018595675.2_ASM1859567v2_genomic.fna/target_genomes.txt --output GCF_018595675.2_ASM1859567v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:58,725] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:58,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e3f28b0-2d55-431f-a268-4d782eea3eba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:58,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e3f28b0-2d55-431f-a268-4d782eea3eba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:58,734] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:45:58,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:58,734] [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
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	100.0	1667	1667	95	conclusive
Flavihumibacter profundi	strain=KCTC 62290	GCA_020076305.1	2716883	2716883	type	True	79.4948	711	1667	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	77.7514	332	1667	95	below_threshold
Flavihumibacter solisilvae	strain=3-3	GCA_000814475.1	1349421	1349421	type	True	77.4713	254	1667	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	77.2663	225	1667	95	below_threshold
Flavihumibacter petaseus	strain=NBRC 106054	GCA_000974785.1	549295	549295	type	True	77.1526	251	1667	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	77.071	257	1667	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.2056	72	1667	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.19	58	1667	95	below_threshold
Lacibacter cauensis	strain=CGMCC 1.7271	GCA_007830055.1	510947	510947	type	True	76.1077	89	1667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:58,735] [INFO] DFAST Taxonomy check result was written to GCF_018595675.2_ASM1859567v2_genomic.fna/tc_result.tsv
[2024-01-25 19:45:58,736] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:58,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:58,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e3f28b0-2d55-431f-a268-4d782eea3eba/dqc_reference/checkm_data
[2024-01-25 19:45:58,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:58,784] [INFO] Task started: CheckM
[2024-01-25 19:45:58,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018595675.2_ASM1859567v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018595675.2_ASM1859567v2_genomic.fna/checkm_input GCF_018595675.2_ASM1859567v2_genomic.fna/checkm_result
[2024-01-25 19:46:58,287] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:58,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:58,308] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:58,309] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:58,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018595675.2_ASM1859567v2_genomic.fna/markers.fasta)
[2024-01-25 19:46:58,310] [INFO] Task started: Blastn
[2024-01-25 19:46:58,310] [INFO] Running command: blastn -query GCF_018595675.2_ASM1859567v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3f28b0-2d55-431f-a268-4d782eea3eba/dqc_reference/reference_markers_gtdb.fasta -out GCF_018595675.2_ASM1859567v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:59,090] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:59,093] [INFO] Selected 18 target genomes.
[2024-01-25 19:46:59,093] [INFO] Target genome list was writen to GCF_018595675.2_ASM1859567v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:59,113] [INFO] Task started: fastANI
[2024-01-25 19:46:59,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgc52b35d4-c2b3-4825-a941-21edc6583517/GCF_018595675.2_ASM1859567v2_genomic.fna.gz --refList GCF_018595675.2_ASM1859567v2_genomic.fna/target_genomes_gtdb.txt --output GCF_018595675.2_ASM1859567v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:14,251] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:14,261] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:14,261] [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_018595675.1	s__Flavihumibacter sp018595675	99.999	1666	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014332695.1	s__Flavihumibacter stibioxidans	77.7386	332	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814475.1	s__Flavihumibacter solisilvae	77.4488	254	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814325.1	s__Flavihumibacter sp000814325	77.4444	246	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001601815.1	s__Flavihumibacter sp001601815	77.4094	221	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483205.1	s__Flavihumibacter sp002483205	77.1847	225	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974785.1	s__Flavihumibacter petaseus	77.1475	249	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787265.1	s__Flavihumibacter sp016787265	77.1039	237	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628535.1	s__Flavisolibacter nicotianae	76.1808	57	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873345.1	s__Flavitalea sp014873345	76.1428	59	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830055.1	s__Lacibacter cauensis	76.1008	88	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963365.1	s__AWTP1-9 sp003963365	75.9891	67	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	75.9122	112	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCA_002336115.1	s__Lacibacter sp002336115	75.6865	54	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	99.94	99.94	0.95	0.95	2	-
GCA_014379345.1	s__Flavitalea sp014379345	75.346	54	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267575.1	s__Puia sp018267575	75.2164	65	1667	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:14,263] [INFO] GTDB search result was written to GCF_018595675.2_ASM1859567v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:14,263] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:14,266] [INFO] DFAST_QC result json was written to GCF_018595675.2_ASM1859567v2_genomic.fna/dqc_result.json
[2024-01-25 19:47:14,266] [INFO] DFAST_QC completed!
[2024-01-25 19:47:14,266] [INFO] Total running time: 0h1m53s