[2024-01-25 19:34:20,970] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:20,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:20,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a1b58ea-349c-419a-8baa-02b2c67184a7/dqc_reference
[2024-01-25 19:34:22,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,075] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,076] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe3ac882-ccc2-4beb-a56d-f9016c4bccdb/GCF_002954345.1_ASM295434v1_genomic.fna.gz | prodigal -d GCF_002954345.1_ASM295434v1_genomic.fna/cds.fna -a GCF_002954345.1_ASM295434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:30,751] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:30,751] [INFO] Task started: HMMsearch
[2024-01-25 19:34:30,752] [INFO] Running command: hmmsearch --tblout GCF_002954345.1_ASM295434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a1b58ea-349c-419a-8baa-02b2c67184a7/dqc_reference/reference_markers.hmm GCF_002954345.1_ASM295434v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:30,952] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:30,953] [INFO] Found 6/6 markers.
[2024-01-25 19:34:30,980] [INFO] Query marker FASTA was written to GCF_002954345.1_ASM295434v1_genomic.fna/markers.fasta
[2024-01-25 19:34:30,980] [INFO] Task started: Blastn
[2024-01-25 19:34:30,980] [INFO] Running command: blastn -query GCF_002954345.1_ASM295434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a1b58ea-349c-419a-8baa-02b2c67184a7/dqc_reference/reference_markers.fasta -out GCF_002954345.1_ASM295434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:31,558] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:31,567] [INFO] Selected 14 target genomes.
[2024-01-25 19:34:31,568] [INFO] Target genome list was writen to GCF_002954345.1_ASM295434v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:31,572] [INFO] Task started: fastANI
[2024-01-25 19:34:31,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe3ac882-ccc2-4beb-a56d-f9016c4bccdb/GCF_002954345.1_ASM295434v1_genomic.fna.gz --refList GCF_002954345.1_ASM295434v1_genomic.fna/target_genomes.txt --output GCF_002954345.1_ASM295434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:41,063] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:41,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a1b58ea-349c-419a-8baa-02b2c67184a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:41,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a1b58ea-349c-419a-8baa-02b2c67184a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:41,072] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:34:41,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:41,072] [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 xylanidelens	strain=DSM 16809	GCA_002954345.1	191564	191564	type	True	100.0	1154	1176	95	conclusive
Nonlabens xylanidelens	strain=DSM 16809	GCA_002934445.1	191564	191564	type	True	99.9856	1079	1176	95	conclusive
Nonlabens dokdonensis	strain=DSW-6	GCA_000332115.1	328515	328515	type	True	79.7468	554	1176	95	below_threshold
Nonlabens dokdonensis	strain=DSM 17205	GCA_003254015.1	328515	328515	type	True	79.7295	554	1176	95	below_threshold
Nonlabens ulvanivorans	strain=PLR	GCA_000732625.1	906888	906888	type	True	79.685	397	1176	95	below_threshold
Nonlabens ulvanivorans	strain=DSM 22727	GCA_003001855.1	906888	906888	type	True	79.6501	403	1176	95	below_threshold
Nonlabens arenilitoris	strain=KCTC 32109	GCA_002954765.1	1217969	1217969	type	True	79.4942	405	1176	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.8962	67	1176	95	below_threshold
Nonlabens spongiae	strain=JCM 13191	GCA_002117125.1	331648	331648	type	True	77.2381	141	1176	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.1805	60	1176	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.5081	67	1176	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	75.9608	56	1176	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.9504	55	1176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:41,075] [INFO] DFAST Taxonomy check result was written to GCF_002954345.1_ASM295434v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:41,075] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:41,075] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:41,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a1b58ea-349c-419a-8baa-02b2c67184a7/dqc_reference/checkm_data
[2024-01-25 19:34:41,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:41,112] [INFO] Task started: CheckM
[2024-01-25 19:34:41,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954345.1_ASM295434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954345.1_ASM295434v1_genomic.fna/checkm_input GCF_002954345.1_ASM295434v1_genomic.fna/checkm_result
[2024-01-25 19:35:09,312] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:09,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:09,333] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:09,334] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:09,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954345.1_ASM295434v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:09,335] [INFO] Task started: Blastn
[2024-01-25 19:35:09,335] [INFO] Running command: blastn -query GCF_002954345.1_ASM295434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a1b58ea-349c-419a-8baa-02b2c67184a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954345.1_ASM295434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:10,157] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:10,160] [INFO] Selected 8 target genomes.
[2024-01-25 19:35:10,160] [INFO] Target genome list was writen to GCF_002954345.1_ASM295434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:10,164] [INFO] Task started: fastANI
[2024-01-25 19:35:10,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe3ac882-ccc2-4beb-a56d-f9016c4bccdb/GCF_002954345.1_ASM295434v1_genomic.fna.gz --refList GCF_002954345.1_ASM295434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954345.1_ASM295434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:15,898] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:15,904] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:15,904] [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_002934445.1	s__Nonlabens xylanidelens	99.9856	1079	1176	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_012974865.1	s__Nonlabens sp012974865	79.7518	553	1176	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332115.1	s__Nonlabens dokdonensis	79.7515	554	1176	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002831625.1	s__Nonlabens sp002831625	79.659	547	1176	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162835.1	s__Nonlabens dokdonensis_B	79.5825	477	1176	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954765.1	s__Nonlabens arenilitoris	79.4524	404	1176	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401815.1	s__Nonlabens sp018401815	79.1734	445	1176	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	99.14	99.12	0.97	0.97	3	-
GCF_002117125.1	s__Nonlabens spongiae	77.2372	141	1176	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Nonlabens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:15,907] [INFO] GTDB search result was written to GCF_002954345.1_ASM295434v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:15,908] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:15,911] [INFO] DFAST_QC result json was written to GCF_002954345.1_ASM295434v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:15,911] [INFO] DFAST_QC completed!
[2024-01-25 19:35:15,911] [INFO] Total running time: 0h0m55s