[2024-01-24 13:36:45,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg35ac6c19-2458-4f0d-a8be-f35d5c0c85c3/dqc_reference
[2024-01-24 13:36:46,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,869] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg04db05a1-e702-4f52-a553-88ea9e1cf234/GCF_000400265.1_ASM40026v1_genomic.fna.gz | prodigal -d GCF_000400265.1_ASM40026v1_genomic.fna/cds.fna -a GCF_000400265.1_ASM40026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:56,670] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:56,670] [INFO] Task started: HMMsearch
[2024-01-24 13:36:56,670] [INFO] Running command: hmmsearch --tblout GCF_000400265.1_ASM40026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35ac6c19-2458-4f0d-a8be-f35d5c0c85c3/dqc_reference/reference_markers.hmm GCF_000400265.1_ASM40026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:57,003] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:57,004] [INFO] Found 6/6 markers.
[2024-01-24 13:36:57,052] [INFO] Query marker FASTA was written to GCF_000400265.1_ASM40026v1_genomic.fna/markers.fasta
[2024-01-24 13:36:57,052] [INFO] Task started: Blastn
[2024-01-24 13:36:57,053] [INFO] Running command: blastn -query GCF_000400265.1_ASM40026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35ac6c19-2458-4f0d-a8be-f35d5c0c85c3/dqc_reference/reference_markers.fasta -out GCF_000400265.1_ASM40026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:57,898] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:57,903] [INFO] Selected 12 target genomes.
[2024-01-24 13:36:57,904] [INFO] Target genome list was writen to GCF_000400265.1_ASM40026v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:57,912] [INFO] Task started: fastANI
[2024-01-24 13:36:57,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg04db05a1-e702-4f52-a553-88ea9e1cf234/GCF_000400265.1_ASM40026v1_genomic.fna.gz --refList GCF_000400265.1_ASM40026v1_genomic.fna/target_genomes.txt --output GCF_000400265.1_ASM40026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:09,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:09,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35ac6c19-2458-4f0d-a8be-f35d5c0c85c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:09,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35ac6c19-2458-4f0d-a8be-f35d5c0c85c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:09,151] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:09,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:09,151] [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 azureus	strain=NBRC 104587	GCA_000400265.1	512649	512649	type	True	100.0	1342	1358	95	conclusive
Vibrio azureus	strain=LC2-005	GCA_002849855.1	512649	512649	type	True	99.9975	1357	1358	95	conclusive
Vibrio azureus	strain=NBRC 104587	GCA_000467165.1	512649	512649	type	True	99.9475	1316	1358	95	conclusive
Vibrio sagamiensis	strain=NBRC 104589	GCA_000400425.1	512650	512650	type	True	91.2338	1050	1358	95	below_threshold
Vibrio sagamiensis	strain=NBRC 104589	GCA_007990935.1	512650	512650	type	True	91.1345	1051	1358	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	82.0324	472	1358	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	81.6271	452	1358	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	80.3664	416	1358	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.8947	258	1358	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.874	259	1358	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.4298	295	1358	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.3428	271	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:09,165] [INFO] DFAST Taxonomy check result was written to GCF_000400265.1_ASM40026v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:09,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:09,166] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:09,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35ac6c19-2458-4f0d-a8be-f35d5c0c85c3/dqc_reference/checkm_data
[2024-01-24 13:37:09,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:09,213] [INFO] Task started: CheckM
[2024-01-24 13:37:09,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000400265.1_ASM40026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000400265.1_ASM40026v1_genomic.fna/checkm_input GCF_000400265.1_ASM40026v1_genomic.fna/checkm_result
[2024-01-24 13:37:47,007] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:47,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:47,029] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:47,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:47,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000400265.1_ASM40026v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:47,030] [INFO] Task started: Blastn
[2024-01-24 13:37:47,031] [INFO] Running command: blastn -query GCF_000400265.1_ASM40026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35ac6c19-2458-4f0d-a8be-f35d5c0c85c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000400265.1_ASM40026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:48,318] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:48,321] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:48,321] [INFO] Target genome list was writen to GCF_000400265.1_ASM40026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:48,334] [INFO] Task started: fastANI
[2024-01-24 13:37:48,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg04db05a1-e702-4f52-a553-88ea9e1cf234/GCF_000400265.1_ASM40026v1_genomic.fna.gz --refList GCF_000400265.1_ASM40026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000400265.1_ASM40026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:59,162] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:59,172] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:59,172] [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_002849855.1	s__Vibrio azureus	99.9975	1357	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_007990935.1	s__Vibrio sagamiensis	91.1164	1052	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.95	99.91	0.97	0.96	3	-
GCF_002163755.1	s__Vibrio campbellii	82.2337	485	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_002741985.1	s__Vibrio rotiferianus	81.6271	452	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_001591145.1	s__Vibrio harveyi	81.6008	474	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_000817815.1	s__Vibrio owensii	81.4572	483	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_000400365.1	s__Vibrio jasicida	81.3246	483	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002906655.1	s__Vibrio hyugaensis	81.1873	492	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_003544875.1	s__Vibrio alfacsensis	80.9882	442	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.49	96.49	0.89	0.89	2	-
GCF_002608565.1	s__Vibrio sp002608565	80.8853	446	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.42	99.42	0.94	0.94	2	-
GCF_000830505.1	s__Vibrio mytili	80.1644	365	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:59,174] [INFO] GTDB search result was written to GCF_000400265.1_ASM40026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:59,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:59,178] [INFO] DFAST_QC result json was written to GCF_000400265.1_ASM40026v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:59,178] [INFO] DFAST_QC completed!
[2024-01-24 13:37:59,178] [INFO] Total running time: 0h1m14s