[2024-01-24 14:56:17,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:17,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:17,964] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf52a531-cb71-4147-a569-1f28b5258305/dqc_reference
[2024-01-24 14:56:19,170] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:19,171] [INFO] Task started: Prodigal
[2024-01-24 14:56:19,171] [INFO] Running command: gunzip -c /var/lib/cwl/stge873cd82-17af-4ce2-a9c1-ef643e8dff87/GCF_019670105.1_ASM1967010v1_genomic.fna.gz | prodigal -d GCF_019670105.1_ASM1967010v1_genomic.fna/cds.fna -a GCF_019670105.1_ASM1967010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:31,556] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:31,556] [INFO] Task started: HMMsearch
[2024-01-24 14:56:31,556] [INFO] Running command: hmmsearch --tblout GCF_019670105.1_ASM1967010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf52a531-cb71-4147-a569-1f28b5258305/dqc_reference/reference_markers.hmm GCF_019670105.1_ASM1967010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:31,861] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:31,862] [INFO] Found 6/6 markers.
[2024-01-24 14:56:31,906] [INFO] Query marker FASTA was written to GCF_019670105.1_ASM1967010v1_genomic.fna/markers.fasta
[2024-01-24 14:56:31,907] [INFO] Task started: Blastn
[2024-01-24 14:56:31,907] [INFO] Running command: blastn -query GCF_019670105.1_ASM1967010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf52a531-cb71-4147-a569-1f28b5258305/dqc_reference/reference_markers.fasta -out GCF_019670105.1_ASM1967010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:32,733] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:32,736] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:32,737] [INFO] Target genome list was writen to GCF_019670105.1_ASM1967010v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:32,760] [INFO] Task started: fastANI
[2024-01-24 14:56:32,761] [INFO] Running command: fastANI --query /var/lib/cwl/stge873cd82-17af-4ce2-a9c1-ef643e8dff87/GCF_019670105.1_ASM1967010v1_genomic.fna.gz --refList GCF_019670105.1_ASM1967010v1_genomic.fna/target_genomes.txt --output GCF_019670105.1_ASM1967010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:43,908] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:43,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf52a531-cb71-4147-a569-1f28b5258305/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:43,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf52a531-cb71-4147-a569-1f28b5258305/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:43,918] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:43,918] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:43,919] [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
Agarivorans albus	strain=JCM 21469	GCA_019670105.1	182262	182262	type	True	100.0	1595	1597	95	conclusive
Agarivorans albus	strain=MKT 106	GCA_000414175.1	182262	182262	type	True	99.967	1537	1597	95	conclusive
Agarivorans litoreus	strain=NBRC 110444	GCA_019649015.1	1510455	1510455	type	True	93.0823	1291	1597	95	below_threshold
Agarivorans aestuarii	strain=KCTC 32543	GCA_019670125.1	1563703	1563703	type	True	92.5534	1360	1597	95	below_threshold
Agarivorans gilvus	strain=WH0801	GCA_001420915.1	680279	680279	type	True	80.3756	586	1597	95	below_threshold
Agarivorans gilvus	strain=CGMCC 1.10131	GCA_014636215.1	680279	680279	type	True	79.9999	573	1597	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.3138	88	1597	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	79.3112	69	1597	95	below_threshold
Vibrio ishigakensis	strain=JCM 19231	GCA_024347675.1	1481914	1481914	type	True	79.0294	66	1597	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	78.2138	92	1597	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:43,920] [INFO] DFAST Taxonomy check result was written to GCF_019670105.1_ASM1967010v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:43,921] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:43,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:43,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf52a531-cb71-4147-a569-1f28b5258305/dqc_reference/checkm_data
[2024-01-24 14:56:43,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:43,971] [INFO] Task started: CheckM
[2024-01-24 14:56:43,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019670105.1_ASM1967010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019670105.1_ASM1967010v1_genomic.fna/checkm_input GCF_019670105.1_ASM1967010v1_genomic.fna/checkm_result
[2024-01-24 14:57:24,252] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:24,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:24,276] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:24,276] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:24,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019670105.1_ASM1967010v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:24,277] [INFO] Task started: Blastn
[2024-01-24 14:57:24,277] [INFO] Running command: blastn -query GCF_019670105.1_ASM1967010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf52a531-cb71-4147-a569-1f28b5258305/dqc_reference/reference_markers_gtdb.fasta -out GCF_019670105.1_ASM1967010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:25,417] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:25,420] [INFO] Selected 8 target genomes.
[2024-01-24 14:57:25,420] [INFO] Target genome list was writen to GCF_019670105.1_ASM1967010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:25,426] [INFO] Task started: fastANI
[2024-01-24 14:57:25,426] [INFO] Running command: fastANI --query /var/lib/cwl/stge873cd82-17af-4ce2-a9c1-ef643e8dff87/GCF_019670105.1_ASM1967010v1_genomic.fna.gz --refList GCF_019670105.1_ASM1967010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019670105.1_ASM1967010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:33,124] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:33,131] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:33,131] [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_000414175.1	s__Agarivorans albus	99.967	1537	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	96.96	96.96	0.93	0.93	2	conclusive
GCF_900537085.1	s__Agarivorans sp900537085	86.9178	1298	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405585.1	s__Agarivorans sp005405585	82.0704	927	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420915.1	s__Agarivorans gilvus	80.4211	589	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	77.7046	65	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_000429505.1	s__Aliagarivorans taiwanensis	77.4662	167	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Aliagarivorans	95.1281	N/A	N/A	N/A	N/A	1	-
GCF_000429485.1	s__Aliagarivorans marinus	77.4595	169	1597	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Aliagarivorans	95.1281	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:33,133] [INFO] GTDB search result was written to GCF_019670105.1_ASM1967010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:33,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:33,136] [INFO] DFAST_QC result json was written to GCF_019670105.1_ASM1967010v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:33,136] [INFO] DFAST_QC completed!
[2024-01-24 14:57:33,136] [INFO] Total running time: 0h1m15s