[2024-01-24 13:46:18,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,570] [INFO] DQC Reference Directory: /var/lib/cwl/stgd302a068-75c6-415e-9726-b501ad4bf8d3/dqc_reference
[2024-01-24 13:46:20,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:20,022] [INFO] Task started: Prodigal
[2024-01-24 13:46:20,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg89413bca-fb5e-4f21-a51a-d1e4fd4660d1/GCF_014529945.1_ASM1452994v1_genomic.fna.gz | prodigal -d GCF_014529945.1_ASM1452994v1_genomic.fna/cds.fna -a GCF_014529945.1_ASM1452994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:12,283] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:12,284] [INFO] Task started: HMMsearch
[2024-01-24 13:47:12,284] [INFO] Running command: hmmsearch --tblout GCF_014529945.1_ASM1452994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd302a068-75c6-415e-9726-b501ad4bf8d3/dqc_reference/reference_markers.hmm GCF_014529945.1_ASM1452994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:12,686] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:12,687] [INFO] Found 6/6 markers.
[2024-01-24 13:47:12,758] [INFO] Query marker FASTA was written to GCF_014529945.1_ASM1452994v1_genomic.fna/markers.fasta
[2024-01-24 13:47:12,758] [INFO] Task started: Blastn
[2024-01-24 13:47:12,758] [INFO] Running command: blastn -query GCF_014529945.1_ASM1452994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd302a068-75c6-415e-9726-b501ad4bf8d3/dqc_reference/reference_markers.fasta -out GCF_014529945.1_ASM1452994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:13,379] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:13,383] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:13,383] [INFO] Target genome list was writen to GCF_014529945.1_ASM1452994v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:13,395] [INFO] Task started: fastANI
[2024-01-24 13:47:13,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg89413bca-fb5e-4f21-a51a-d1e4fd4660d1/GCF_014529945.1_ASM1452994v1_genomic.fna.gz --refList GCF_014529945.1_ASM1452994v1_genomic.fna/target_genomes.txt --output GCF_014529945.1_ASM1452994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:28,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:28,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd302a068-75c6-415e-9726-b501ad4bf8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:28,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd302a068-75c6-415e-9726-b501ad4bf8d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:28,642] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:28,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:28,642] [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
Chitinophaga varians	strain=KACC 19415	GCA_014529945.1	2202339	2202339	type	True	100.0	2881	2884	95	conclusive
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	89.2993	2401	2884	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	85.5939	2071	2884	95	below_threshold
Chitinophaga eiseniae	strain=DSM 22224	GCA_900167135.1	634771	634771	type	True	85.4695	2113	2884	95	below_threshold
Chitinophaga qingshengii	strain=JCM 30026	GCA_014529935.1	1569794	1569794	type	True	84.1049	1883	2884	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	79.2821	855	2884	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:28,644] [INFO] DFAST Taxonomy check result was written to GCF_014529945.1_ASM1452994v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:28,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:28,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:28,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd302a068-75c6-415e-9726-b501ad4bf8d3/dqc_reference/checkm_data
[2024-01-24 13:47:28,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:28,724] [INFO] Task started: CheckM
[2024-01-24 13:47:28,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014529945.1_ASM1452994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014529945.1_ASM1452994v1_genomic.fna/checkm_input GCF_014529945.1_ASM1452994v1_genomic.fna/checkm_result
[2024-01-24 13:49:38,355] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:38,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:38,382] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:38,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:38,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014529945.1_ASM1452994v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:38,383] [INFO] Task started: Blastn
[2024-01-24 13:49:38,383] [INFO] Running command: blastn -query GCF_014529945.1_ASM1452994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd302a068-75c6-415e-9726-b501ad4bf8d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014529945.1_ASM1452994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:39,279] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:39,282] [INFO] Selected 6 target genomes.
[2024-01-24 13:49:39,282] [INFO] Target genome list was writen to GCF_014529945.1_ASM1452994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:39,291] [INFO] Task started: fastANI
[2024-01-24 13:49:39,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg89413bca-fb5e-4f21-a51a-d1e4fd4660d1/GCF_014529945.1_ASM1452994v1_genomic.fna.gz --refList GCF_014529945.1_ASM1452994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014529945.1_ASM1452994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:54,289] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:54,296] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:54,296] [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_014529945.1	s__Chitinophaga varians	100.0	2881	2884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012927205.1	s__Chitinophaga fulva	89.2976	2401	2884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641275.1	s__Chitinophaga varians_A	87.9473	2279	2884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012516355.1	s__Chitinophaga sp012516355	85.5473	2054	2884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	99.48	99.48	0.97	0.97	2	-
GCF_900167135.1	s__Chitinophaga eiseniae	85.4695	2113	2884	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	84.1009	1884	2884	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 13:49:54,297] [INFO] GTDB search result was written to GCF_014529945.1_ASM1452994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:54,298] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:54,300] [INFO] DFAST_QC result json was written to GCF_014529945.1_ASM1452994v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:54,301] [INFO] DFAST_QC completed!
[2024-01-24 13:49:54,301] [INFO] Total running time: 0h3m36s