[2024-01-24 11:51:19,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:19,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:19,561] [INFO] DQC Reference Directory: /var/lib/cwl/stgce58c53b-55e4-4502-9537-3a125d533230/dqc_reference
[2024-01-24 11:51:20,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:20,788] [INFO] Task started: Prodigal
[2024-01-24 11:51:20,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg171093a7-05dd-45aa-b634-fe724e8aa4bd/GCF_009938165.1_ASM993816v1_genomic.fna.gz | prodigal -d GCF_009938165.1_ASM993816v1_genomic.fna/cds.fna -a GCF_009938165.1_ASM993816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:31,458] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:31,459] [INFO] Task started: HMMsearch
[2024-01-24 11:51:31,459] [INFO] Running command: hmmsearch --tblout GCF_009938165.1_ASM993816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce58c53b-55e4-4502-9537-3a125d533230/dqc_reference/reference_markers.hmm GCF_009938165.1_ASM993816v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:31,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:31,738] [INFO] Found 6/6 markers.
[2024-01-24 11:51:31,776] [INFO] Query marker FASTA was written to GCF_009938165.1_ASM993816v1_genomic.fna/markers.fasta
[2024-01-24 11:51:31,777] [INFO] Task started: Blastn
[2024-01-24 11:51:31,777] [INFO] Running command: blastn -query GCF_009938165.1_ASM993816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce58c53b-55e4-4502-9537-3a125d533230/dqc_reference/reference_markers.fasta -out GCF_009938165.1_ASM993816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:32,552] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:32,560] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:32,560] [INFO] Target genome list was writen to GCF_009938165.1_ASM993816v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:32,597] [INFO] Task started: fastANI
[2024-01-24 11:51:32,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg171093a7-05dd-45aa-b634-fe724e8aa4bd/GCF_009938165.1_ASM993816v1_genomic.fna.gz --refList GCF_009938165.1_ASM993816v1_genomic.fna/target_genomes.txt --output GCF_009938165.1_ASM993816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:48,175] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:48,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce58c53b-55e4-4502-9537-3a125d533230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:48,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce58c53b-55e4-4502-9537-3a125d533230/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:48,188] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:48,188] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:48,189] [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
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	83.0476	762	1434	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	82.6497	768	1434	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	82.1304	721	1434	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	82.0339	720	1434	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	81.3116	669	1434	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	80.9462	409	1434	95	below_threshold
Vibrio alginolyticus	strain=ATCC 17749	GCA_000354175.2	663	663	type	True	80.8827	404	1434	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	80.8167	405	1434	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.8052	395	1434	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	80.6752	585	1434	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	80.6457	625	1434	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.5678	359	1434	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	80.4452	572	1434	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	80.2156	393	1434	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	80.2154	394	1434	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.1605	367	1434	95	below_threshold
Thaumasiovibrio occultus	strain=C4II189	GCA_019703815.1	1891184	1891184	type	True	80.0333	193	1434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:48,190] [INFO] DFAST Taxonomy check result was written to GCF_009938165.1_ASM993816v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:48,191] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:48,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:48,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce58c53b-55e4-4502-9537-3a125d533230/dqc_reference/checkm_data
[2024-01-24 11:51:48,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:48,233] [INFO] Task started: CheckM
[2024-01-24 11:51:48,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009938165.1_ASM993816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009938165.1_ASM993816v1_genomic.fna/checkm_input GCF_009938165.1_ASM993816v1_genomic.fna/checkm_result
[2024-01-24 11:52:24,092] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:24,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:24,113] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:24,113] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:24,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009938165.1_ASM993816v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:24,114] [INFO] Task started: Blastn
[2024-01-24 11:52:24,114] [INFO] Running command: blastn -query GCF_009938165.1_ASM993816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce58c53b-55e4-4502-9537-3a125d533230/dqc_reference/reference_markers_gtdb.fasta -out GCF_009938165.1_ASM993816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:25,231] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:25,235] [INFO] Selected 10 target genomes.
[2024-01-24 11:52:25,236] [INFO] Target genome list was writen to GCF_009938165.1_ASM993816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:25,245] [INFO] Task started: fastANI
[2024-01-24 11:52:25,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg171093a7-05dd-45aa-b634-fe724e8aa4bd/GCF_009938165.1_ASM993816v1_genomic.fna.gz --refList GCF_009938165.1_ASM993816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009938165.1_ASM993816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:34,468] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:34,486] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:34,487] [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_009938165.1	s__Vibrio taketomensis	100.0	1434	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	conclusive
GCF_009938225.1	s__Vibrio ponticus	83.0698	760	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_003350325.1	s__Vibrio rhodolitus	82.6709	768	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_015278125.1	s__Vibrio sp015278125	82.4686	749	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938205.1	s__Vibrio panuliri	82.1058	727	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_000222585.1	s__Vibrio scophthalmi	80.64	626	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_011806575.1	s__Vibrio hepatarius_A	80.4421	412	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_001591105.1	s__Vibrio nereis	80.2049	395	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001274785.1	s__Vibrio hepatarius	80.1828	429	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_002157795.1	s__Thaumasiovibrio occultus	78.7949	180	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Thaumasiovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:34,489] [INFO] GTDB search result was written to GCF_009938165.1_ASM993816v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:34,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:34,495] [INFO] DFAST_QC result json was written to GCF_009938165.1_ASM993816v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:34,495] [INFO] DFAST_QC completed!
[2024-01-24 11:52:34,495] [INFO] Total running time: 0h1m15s