[2024-01-24 12:27:18,741] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:18,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:18,743] [INFO] DQC Reference Directory: /var/lib/cwl/stgb787207c-c5cc-4a82-9f6b-d82a77908985/dqc_reference
[2024-01-24 12:27:19,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:19,916] [INFO] Task started: Prodigal
[2024-01-24 12:27:19,917] [INFO] Running command: gunzip -c /var/lib/cwl/stga452b274-8d72-4b8b-aed5-e70cfda8cd9a/GCF_003332885.2_ASM333288v2_genomic.fna.gz | prodigal -d GCF_003332885.2_ASM333288v2_genomic.fna/cds.fna -a GCF_003332885.2_ASM333288v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:51,132] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:51,133] [INFO] Task started: HMMsearch
[2024-01-24 12:27:51,133] [INFO] Running command: hmmsearch --tblout GCF_003332885.2_ASM333288v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb787207c-c5cc-4a82-9f6b-d82a77908985/dqc_reference/reference_markers.hmm GCF_003332885.2_ASM333288v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:51,376] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:51,377] [INFO] Found 6/6 markers.
[2024-01-24 12:27:51,416] [INFO] Query marker FASTA was written to GCF_003332885.2_ASM333288v2_genomic.fna/markers.fasta
[2024-01-24 12:27:51,416] [INFO] Task started: Blastn
[2024-01-24 12:27:51,417] [INFO] Running command: blastn -query GCF_003332885.2_ASM333288v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb787207c-c5cc-4a82-9f6b-d82a77908985/dqc_reference/reference_markers.fasta -out GCF_003332885.2_ASM333288v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:51,993] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:51,996] [INFO] Selected 19 target genomes.
[2024-01-24 12:27:51,996] [INFO] Target genome list was writen to GCF_003332885.2_ASM333288v2_genomic.fna/target_genomes.txt
[2024-01-24 12:27:52,006] [INFO] Task started: fastANI
[2024-01-24 12:27:52,006] [INFO] Running command: fastANI --query /var/lib/cwl/stga452b274-8d72-4b8b-aed5-e70cfda8cd9a/GCF_003332885.2_ASM333288v2_genomic.fna.gz --refList GCF_003332885.2_ASM333288v2_genomic.fna/target_genomes.txt --output GCF_003332885.2_ASM333288v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:07,870] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:07,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb787207c-c5cc-4a82-9f6b-d82a77908985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:07,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb787207c-c5cc-4a82-9f6b-d82a77908985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:07,882] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:28:07,883] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:28:07,883] [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
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	78.5012	564	1633	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	78.4715	567	1633	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.8851	248	1633	95	below_threshold
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	76.6411	174	1633	95	below_threshold
Flavisolibacter ginsenosidimutans	strain=Gsoil 636	GCA_007970805.1	661481	661481	type	True	76.6152	204	1633	95	below_threshold
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	76.5513	180	1633	95	below_threshold
Phnomibacter ginsenosidimutans	strain=SB-02	GCA_009740285.1	2676868	2676868	type	True	76.5467	122	1633	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.5103	61	1633	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.4966	102	1633	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.3644	102	1633	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	76.1442	118	1633	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	76.0287	92	1633	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.0109	93	1633	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	75.9884	107	1633	95	below_threshold
Chitinophaga japonensis	strain=DSM 13484	GCA_007830125.1	104662	104662	type	True	75.7481	94	1633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:07,884] [INFO] DFAST Taxonomy check result was written to GCF_003332885.2_ASM333288v2_genomic.fna/tc_result.tsv
[2024-01-24 12:28:07,885] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:07,885] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:07,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb787207c-c5cc-4a82-9f6b-d82a77908985/dqc_reference/checkm_data
[2024-01-24 12:28:07,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:07,932] [INFO] Task started: CheckM
[2024-01-24 12:28:07,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003332885.2_ASM333288v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003332885.2_ASM333288v2_genomic.fna/checkm_input GCF_003332885.2_ASM333288v2_genomic.fna/checkm_result
[2024-01-24 12:29:27,985] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:27,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:28,006] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:28,006] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:28,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003332885.2_ASM333288v2_genomic.fna/markers.fasta)
[2024-01-24 12:29:28,007] [INFO] Task started: Blastn
[2024-01-24 12:29:28,007] [INFO] Running command: blastn -query GCF_003332885.2_ASM333288v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb787207c-c5cc-4a82-9f6b-d82a77908985/dqc_reference/reference_markers_gtdb.fasta -out GCF_003332885.2_ASM333288v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:28,769] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:28,773] [INFO] Selected 16 target genomes.
[2024-01-24 12:29:28,773] [INFO] Target genome list was writen to GCF_003332885.2_ASM333288v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:28,799] [INFO] Task started: fastANI
[2024-01-24 12:29:28,799] [INFO] Running command: fastANI --query /var/lib/cwl/stga452b274-8d72-4b8b-aed5-e70cfda8cd9a/GCF_003332885.2_ASM333288v2_genomic.fna.gz --refList GCF_003332885.2_ASM333288v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003332885.2_ASM333288v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:42,284] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:42,297] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:42,297] [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_003332885.2	s__Paracnuella aquatica	100.0	1630	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	conclusive
GCF_001953305.1	s__Cnuella takakiae	78.5085	563	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Cnuella	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013327885.1	s__Flavisolibacter sp013327885	77.6462	310	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014163555.1	s__Flavisolibacter sp014163555	77.0014	265	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628535.1	s__Flavisolibacter nicotianae	76.8851	248	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343705.1	s__Flaviaesturariibacter aridisoli	76.6411	174	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970805.1	s__Flavisolibacter ginsenosidimutans	76.6152	204	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337505.1	s__Flaviaesturariibacter flavus	76.5615	179	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009740285.1	s__Phnomibacter ginsenosidimutans	76.5614	120	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Phnomibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	76.3644	102	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016192105.1	s__JJ008 sp016192105	76.1952	84	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786725.1	s__Ferruginibacter sp016786725	76.1303	59	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003412455.1	s__Deminuibacter soli	76.1011	132	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Deminuibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970185.1	s__Pseudobacter ginsenosidimutans	76.0109	93	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011759375.1	s__Paraflavitalea devenefica	75.9884	107	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:42,299] [INFO] GTDB search result was written to GCF_003332885.2_ASM333288v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:42,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:42,306] [INFO] DFAST_QC result json was written to GCF_003332885.2_ASM333288v2_genomic.fna/dqc_result.json
[2024-01-24 12:29:42,306] [INFO] DFAST_QC completed!
[2024-01-24 12:29:42,307] [INFO] Total running time: 0h2m24s