[2024-01-24 14:54:56,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fc4b703-994c-4079-be72-27238ccf4abb/dqc_reference
[2024-01-24 14:54:57,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,790] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgd581b5bf-9708-481a-ab83-a717fde5f79d/GCF_002994045.1_ASM299404v1_genomic.fna.gz | prodigal -d GCF_002994045.1_ASM299404v1_genomic.fna/cds.fna -a GCF_002994045.1_ASM299404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:13,382] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:13,383] [INFO] Task started: HMMsearch
[2024-01-24 14:55:13,383] [INFO] Running command: hmmsearch --tblout GCF_002994045.1_ASM299404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fc4b703-994c-4079-be72-27238ccf4abb/dqc_reference/reference_markers.hmm GCF_002994045.1_ASM299404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:13,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:13,669] [INFO] Found 6/6 markers.
[2024-01-24 14:55:13,702] [INFO] Query marker FASTA was written to GCF_002994045.1_ASM299404v1_genomic.fna/markers.fasta
[2024-01-24 14:55:13,703] [INFO] Task started: Blastn
[2024-01-24 14:55:13,703] [INFO] Running command: blastn -query GCF_002994045.1_ASM299404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fc4b703-994c-4079-be72-27238ccf4abb/dqc_reference/reference_markers.fasta -out GCF_002994045.1_ASM299404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:14,326] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:14,329] [INFO] Selected 17 target genomes.
[2024-01-24 14:55:14,329] [INFO] Target genome list was writen to GCF_002994045.1_ASM299404v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:14,335] [INFO] Task started: fastANI
[2024-01-24 14:55:14,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgd581b5bf-9708-481a-ab83-a717fde5f79d/GCF_002994045.1_ASM299404v1_genomic.fna.gz --refList GCF_002994045.1_ASM299404v1_genomic.fna/target_genomes.txt --output GCF_002994045.1_ASM299404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:27,774] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:27,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fc4b703-994c-4079-be72-27238ccf4abb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:27,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fc4b703-994c-4079-be72-27238ccf4abb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:27,786] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:27,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:27,787] [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
Nonlabens agnitus	strain=JCM 17109	GCA_002994045.1	870484	870484	type	True	100.0	1066	1069	95	conclusive
Nonlabens marinus	strain=S1-08	GCA_000831385.1	930802	930802	type	True	78.8045	410	1069	95	below_threshold
Nonlabens antarcticus	strain=JCM 14068	GCA_015356755.1	392714	392714	type	True	78.2351	344	1069	95	below_threshold
Nonlabens ponticola	strain=MJ115	GCA_003966335.1	2496866	2496866	type	True	78.1542	318	1069	95	below_threshold
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	77.6183	213	1069	95	below_threshold
Nonlabens ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	77.5282	161	1069	95	below_threshold
Nonlabens xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	77.4832	176	1069	95	below_threshold
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	77.4355	174	1069	95	below_threshold
Nonlabens ulvanivorans	strain=DSM 22727	GCA_003001855.1	906888	906888	type	True	77.3978	163	1069	95	below_threshold
Nonlabens spongiae	strain=JCM 13191	GCA_002117125.1	331648	331648	type	True	77.0944	149	1069	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	75.9689	55	1069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:27,788] [INFO] DFAST Taxonomy check result was written to GCF_002994045.1_ASM299404v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:27,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:27,789] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:27,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fc4b703-994c-4079-be72-27238ccf4abb/dqc_reference/checkm_data
[2024-01-24 14:55:27,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:27,826] [INFO] Task started: CheckM
[2024-01-24 14:55:27,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002994045.1_ASM299404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002994045.1_ASM299404v1_genomic.fna/checkm_input GCF_002994045.1_ASM299404v1_genomic.fna/checkm_result
[2024-01-24 14:56:14,382] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:14,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:14,403] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:14,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:14,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002994045.1_ASM299404v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:14,404] [INFO] Task started: Blastn
[2024-01-24 14:56:14,405] [INFO] Running command: blastn -query GCF_002994045.1_ASM299404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fc4b703-994c-4079-be72-27238ccf4abb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002994045.1_ASM299404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:15,283] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:15,287] [INFO] Selected 7 target genomes.
[2024-01-24 14:56:15,287] [INFO] Target genome list was writen to GCF_002994045.1_ASM299404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:15,293] [INFO] Task started: fastANI
[2024-01-24 14:56:15,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgd581b5bf-9708-481a-ab83-a717fde5f79d/GCF_002994045.1_ASM299404v1_genomic.fna.gz --refList GCF_002994045.1_ASM299404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002994045.1_ASM299404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:20,638] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:20,650] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:20,650] [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_002994045.1	s__Nonlabens agnitus	100.0	1066	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001413925.1	s__Nonlabens sp001413925	94.74	910	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101765.1	s__Nonlabens sp900101765	80.8776	670	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000831385.1	s__Nonlabens marinus	78.771	407	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356755.1	s__Nonlabens antarcticus	78.2453	343	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966335.1	s__Nonlabens ponticola	78.1696	323	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153385.1	s__Nonlabens sp000153385	77.125	171	1069	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:20,652] [INFO] GTDB search result was written to GCF_002994045.1_ASM299404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:20,652] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:20,656] [INFO] DFAST_QC result json was written to GCF_002994045.1_ASM299404v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:20,656] [INFO] DFAST_QC completed!
[2024-01-24 14:56:20,656] [INFO] Total running time: 0h1m24s