[2024-01-24 13:57:00,660] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c9ffc57-cb25-43dc-ba54-b130cf8d47d2/dqc_reference
[2024-01-24 13:57:02,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,001] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg85fee9bc-d1a1-440e-a21c-91472b2a8aaf/GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/cds.fna -a GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:36,098] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:36,098] [INFO] Task started: HMMsearch
[2024-01-24 13:57:36,099] [INFO] Running command: hmmsearch --tblout GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c9ffc57-cb25-43dc-ba54-b130cf8d47d2/dqc_reference/reference_markers.hmm GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:36,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:36,519] [INFO] Found 6/6 markers.
[2024-01-24 13:57:36,564] [INFO] Query marker FASTA was written to GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:36,565] [INFO] Task started: Blastn
[2024-01-24 13:57:36,565] [INFO] Running command: blastn -query GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c9ffc57-cb25-43dc-ba54-b130cf8d47d2/dqc_reference/reference_markers.fasta -out GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:37,168] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:37,177] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:37,177] [INFO] Target genome list was writen to GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:37,185] [INFO] Task started: fastANI
[2024-01-24 13:57:37,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg85fee9bc-d1a1-440e-a21c-91472b2a8aaf/GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna.gz --refList GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:54,232] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:54,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c9ffc57-cb25-43dc-ba54-b130cf8d47d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:54,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c9ffc57-cb25-43dc-ba54-b130cf8d47d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:54,244] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:54,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:54,245] [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=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	100.0	1869	1870	95	conclusive
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	99.9775	1863	1870	95	conclusive
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	77.2805	201	1870	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.8826	213	1870	95	below_threshold
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	76.8285	205	1870	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.4489	110	1870	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	76.3734	106	1870	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	76.3409	88	1870	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.1782	100	1870	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.9757	126	1870	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	75.9133	134	1870	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.7317	68	1870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,246] [INFO] DFAST Taxonomy check result was written to GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:57:54,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:54,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:54,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c9ffc57-cb25-43dc-ba54-b130cf8d47d2/dqc_reference/checkm_data
[2024-01-24 13:57:54,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:54,307] [INFO] Task started: CheckM
[2024-01-24 13:57:54,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/checkm_input GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:28,271] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:28,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:28,296] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:28,296] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:28,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:28,297] [INFO] Task started: Blastn
[2024-01-24 13:59:28,297] [INFO] Running command: blastn -query GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c9ffc57-cb25-43dc-ba54-b130cf8d47d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:29,122] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:29,126] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:29,127] [INFO] Target genome list was writen to GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:29,142] [INFO] Task started: fastANI
[2024-01-24 13:59:29,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg85fee9bc-d1a1-440e-a21c-91472b2a8aaf/GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna.gz --refList GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:41,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:41,113] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:41,113] [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_001953305.1	s__Cnuella takakiae	99.9775	1863	1870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Cnuella	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_003332885.2	s__Paracnuella aquatica	78.5369	552	1870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	-
GCF_004337505.1	s__Flaviaesturariibacter flavus	77.2805	201	1870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013327885.1	s__Flavisolibacter sp013327885	76.9245	248	1870	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	76.8826	213	1870	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	76.8316	203	1870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173235.1	s__Flaviaesturariibacter sp004173235	76.6062	159	1870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015069695.1	s__JADCRZ01 sp015069695	75.9705	123	1870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JADCRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109685.1	s__Chitinophaga rupis	75.8765	102	1870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014529935.1	s__Chitinophaga qingshengii	75.6083	69	1870	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:41,115] [INFO] GTDB search result was written to GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:41,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:41,119] [INFO] DFAST_QC result json was written to GCF_900129015.1_IMG-taxon_2695420933_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:41,119] [INFO] DFAST_QC completed!
[2024-01-24 13:59:41,119] [INFO] Total running time: 0h2m40s