[2023-06-27 22:54:52,355] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:54:52,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:54:52,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ae95474-8784-48f4-9170-35edca9182c7/dqc_reference
[2023-06-27 22:54:53,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:54:53,725] [INFO] Task started: Prodigal
[2023-06-27 22:54:53,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b391d8d-d201-4529-9f74-c6df7ba0d215/GCA_002336195.1_ASM233619v1_genomic.fna.gz | prodigal -d GCA_002336195.1_ASM233619v1_genomic.fna/cds.fna -a GCA_002336195.1_ASM233619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:55:03,552] [INFO] Task succeeded: Prodigal
[2023-06-27 22:55:03,553] [INFO] Task started: HMMsearch
[2023-06-27 22:55:03,553] [INFO] Running command: hmmsearch --tblout GCA_002336195.1_ASM233619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ae95474-8784-48f4-9170-35edca9182c7/dqc_reference/reference_markers.hmm GCA_002336195.1_ASM233619v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:55:03,794] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:55:03,795] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9b391d8d-d201-4529-9f74-c6df7ba0d215/GCA_002336195.1_ASM233619v1_genomic.fna.gz]
[2023-06-27 22:55:03,833] [INFO] Query marker FASTA was written to GCA_002336195.1_ASM233619v1_genomic.fna/markers.fasta
[2023-06-27 22:55:03,834] [INFO] Task started: Blastn
[2023-06-27 22:55:03,834] [INFO] Running command: blastn -query GCA_002336195.1_ASM233619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ae95474-8784-48f4-9170-35edca9182c7/dqc_reference/reference_markers.fasta -out GCA_002336195.1_ASM233619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:55:04,496] [INFO] Task succeeded: Blastn
[2023-06-27 22:55:04,502] [INFO] Selected 22 target genomes.
[2023-06-27 22:55:04,503] [INFO] Target genome list was writen to GCA_002336195.1_ASM233619v1_genomic.fna/target_genomes.txt
[2023-06-27 22:55:04,505] [INFO] Task started: fastANI
[2023-06-27 22:55:04,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b391d8d-d201-4529-9f74-c6df7ba0d215/GCA_002336195.1_ASM233619v1_genomic.fna.gz --refList GCA_002336195.1_ASM233619v1_genomic.fna/target_genomes.txt --output GCA_002336195.1_ASM233619v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:55:24,045] [INFO] Task succeeded: fastANI
[2023-06-27 22:55:24,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ae95474-8784-48f4-9170-35edca9182c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:55:24,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ae95474-8784-48f4-9170-35edca9182c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:55:24,058] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:55:24,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 22:55:24,059] [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
Roseivirga misakiensis	strain=SK-8	GCA_001747105.1	1563681	1563681	type	True	77.3701	172	753	95	below_threshold
Roseivirga thermotolerans	strain=CGMCC 1.15111	GCA_014653175.1	1758176	1758176	type	True	77.083	58	753	95	below_threshold
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	76.8867	74	753	95	below_threshold
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	76.8034	81	753	95	below_threshold
Roseivirga spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	76.7232	90	753	95	below_threshold
Roseivirga seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	76.7158	74	753	95	below_threshold
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	76.6914	86	753	95	below_threshold
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	76.6902	89	753	95	below_threshold
Roseivirga echinicomitans	strain=KMM 6058	GCA_001592935.1	296218	296218	type	True	76.6169	72	753	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 22:55:24,060] [INFO] DFAST Taxonomy check result was written to GCA_002336195.1_ASM233619v1_genomic.fna/tc_result.tsv
[2023-06-27 22:55:24,061] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:55:24,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:55:24,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ae95474-8784-48f4-9170-35edca9182c7/dqc_reference/checkm_data
[2023-06-27 22:55:24,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:55:24,095] [INFO] Task started: CheckM
[2023-06-27 22:55:24,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002336195.1_ASM233619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002336195.1_ASM233619v1_genomic.fna/checkm_input GCA_002336195.1_ASM233619v1_genomic.fna/checkm_result
[2023-06-27 22:55:58,001] [INFO] Task succeeded: CheckM
[2023-06-27 22:55:58,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:55:58,026] [INFO] ===== Completeness check finished =====
[2023-06-27 22:55:58,026] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:55:58,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002336195.1_ASM233619v1_genomic.fna/markers.fasta)
[2023-06-27 22:55:58,028] [INFO] Task started: Blastn
[2023-06-27 22:55:58,028] [INFO] Running command: blastn -query GCA_002336195.1_ASM233619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ae95474-8784-48f4-9170-35edca9182c7/dqc_reference/reference_markers_gtdb.fasta -out GCA_002336195.1_ASM233619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:55:58,962] [INFO] Task succeeded: Blastn
[2023-06-27 22:55:58,967] [INFO] Selected 13 target genomes.
[2023-06-27 22:55:58,967] [INFO] Target genome list was writen to GCA_002336195.1_ASM233619v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:55:58,968] [INFO] Task started: fastANI
[2023-06-27 22:55:58,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b391d8d-d201-4529-9f74-c6df7ba0d215/GCA_002336195.1_ASM233619v1_genomic.fna.gz --refList GCA_002336195.1_ASM233619v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002336195.1_ASM233619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:56:07,751] [INFO] Task succeeded: fastANI
[2023-06-27 22:56:07,761] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 22:56:07,761] [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
GCA_002477595.1	s__Fabibacter sp002477595	99.7758	542	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	99.68	99.60	0.84	0.83	4	conclusive
GCF_017592825.1	s__Fabibacter sp017592825	79.1059	381	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747095.1	s__Fabibacter sp001747095	78.9362	366	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747105.1	s__Fabibacter misakiensis	77.3537	173	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427755.1	s__Fabibacter sp002427755	76.9905	99	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592965.1	s__Fabibacter spongicola	76.7232	90	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCF_900111145.1	s__Fabibacter pacificus	76.6914	86	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001592935.1	s__Roseivirga echinicomitans	76.6169	72	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 22:56:07,763] [INFO] GTDB search result was written to GCA_002336195.1_ASM233619v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:56:07,764] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:56:07,768] [INFO] DFAST_QC result json was written to GCA_002336195.1_ASM233619v1_genomic.fna/dqc_result.json
[2023-06-27 22:56:07,768] [INFO] DFAST_QC completed!
[2023-06-27 22:56:07,768] [INFO] Total running time: 0h1m15s