[2024-01-24 11:26:37,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:37,806] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:37,807] [INFO] DQC Reference Directory: /var/lib/cwl/stga715157c-3c1c-4646-8cfd-edab4159d823/dqc_reference
[2024-01-24 11:26:39,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,213] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,213] [INFO] Running command: gunzip -c /var/lib/cwl/stg07abf7b8-b358-42f9-8c88-1e03bdaba0de/GCF_024582835.1_ASM2458283v1_genomic.fna.gz | prodigal -d GCF_024582835.1_ASM2458283v1_genomic.fna/cds.fna -a GCF_024582835.1_ASM2458283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:49,668] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:49,668] [INFO] Task started: HMMsearch
[2024-01-24 11:26:49,669] [INFO] Running command: hmmsearch --tblout GCF_024582835.1_ASM2458283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga715157c-3c1c-4646-8cfd-edab4159d823/dqc_reference/reference_markers.hmm GCF_024582835.1_ASM2458283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:49,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:49,967] [INFO] Found 6/6 markers.
[2024-01-24 11:26:50,010] [INFO] Query marker FASTA was written to GCF_024582835.1_ASM2458283v1_genomic.fna/markers.fasta
[2024-01-24 11:26:50,010] [INFO] Task started: Blastn
[2024-01-24 11:26:50,011] [INFO] Running command: blastn -query GCF_024582835.1_ASM2458283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga715157c-3c1c-4646-8cfd-edab4159d823/dqc_reference/reference_markers.fasta -out GCF_024582835.1_ASM2458283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:50,846] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:50,850] [INFO] Selected 23 target genomes.
[2024-01-24 11:26:50,851] [INFO] Target genome list was writen to GCF_024582835.1_ASM2458283v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:50,871] [INFO] Task started: fastANI
[2024-01-24 11:26:50,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg07abf7b8-b358-42f9-8c88-1e03bdaba0de/GCF_024582835.1_ASM2458283v1_genomic.fna.gz --refList GCF_024582835.1_ASM2458283v1_genomic.fna/target_genomes.txt --output GCF_024582835.1_ASM2458283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:10,863] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:10,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga715157c-3c1c-4646-8cfd-edab4159d823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:10,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga715157c-3c1c-4646-8cfd-edab4159d823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:10,886] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:10,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:10,886] [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 nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	83.4796	885	1410	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	83.4544	896	1410	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	82.0598	488	1410	95	below_threshold
Vibrio parahaemolyticus		GCA_001558495.2	670	670	type	True	81.453	506	1410	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	81.2892	520	1410	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	81.2055	556	1410	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	80.9965	552	1410	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	80.9142	482	1410	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.8938	536	1410	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	80.8815	553	1410	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001998785.1	670	670	type	True	80.8659	473	1410	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	80.8593	537	1410	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	80.8382	525	1410	95	below_threshold
Vibrio parahaemolyticus	strain=NBRC 12711	GCA_000813305.1	670	670	type	True	80.8115	475	1410	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.7932	407	1410	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.6458	535	1410	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.5928	400	1410	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	80.5604	406	1410	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	80.5296	444	1410	95	below_threshold
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	80.4783	419	1410	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.4705	411	1410	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	80.3238	438	1410	95	below_threshold
Vibrio algivorus	strain=SA2	GCA_002218005.2	1667024	1667024	type	True	79.3335	218	1410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:10,888] [INFO] DFAST Taxonomy check result was written to GCF_024582835.1_ASM2458283v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:10,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:10,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:10,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga715157c-3c1c-4646-8cfd-edab4159d823/dqc_reference/checkm_data
[2024-01-24 11:27:10,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:10,934] [INFO] Task started: CheckM
[2024-01-24 11:27:10,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024582835.1_ASM2458283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024582835.1_ASM2458283v1_genomic.fna/checkm_input GCF_024582835.1_ASM2458283v1_genomic.fna/checkm_result
[2024-01-24 11:27:46,959] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:46,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:46,979] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:46,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:46,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024582835.1_ASM2458283v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:46,980] [INFO] Task started: Blastn
[2024-01-24 11:27:46,980] [INFO] Running command: blastn -query GCF_024582835.1_ASM2458283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga715157c-3c1c-4646-8cfd-edab4159d823/dqc_reference/reference_markers_gtdb.fasta -out GCF_024582835.1_ASM2458283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:48,153] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:48,158] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:48,158] [INFO] Target genome list was writen to GCF_024582835.1_ASM2458283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:48,173] [INFO] Task started: fastANI
[2024-01-24 11:27:48,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg07abf7b8-b358-42f9-8c88-1e03bdaba0de/GCF_024582835.1_ASM2458283v1_genomic.fna.gz --refList GCF_024582835.1_ASM2458283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024582835.1_ASM2458283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:03,272] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:03,290] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:28:03,291] [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_001591105.1	s__Vibrio nereis	83.4965	886	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011806575.1	s__Vibrio hepatarius_A	83.3093	746	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_001274785.1	s__Vibrio hepatarius	83.273	762	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_900460535.1	s__Vibrio parahaemolyticus	81.3412	521	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.33	97.74	0.94	0.76	1553	-
GCF_000772105.1	s__Vibrio tubiashii	81.187	556	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_002163755.1	s__Vibrio campbellii	81.1036	471	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000808535.1	s__Vibrio sinaloensis	81.0825	566	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_009811315.1	s__Vibrio atypicus	81.0494	576	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_002741985.1	s__Vibrio rotiferianus	80.8969	458	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_003970385.1	s__Vibrio aquaticus	80.8809	538	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176135.1	s__Vibrio coralliilyticus	80.8667	536	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_004551525.1	s__Vibrio ouci	80.6937	569	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775715.1	s__Vibrio tubiashii_A	80.6744	474	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113835.1	s__Vibrio sp013113835	80.5086	534	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350325.1	s__Vibrio rhodolitus	80.4651	420	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_001591145.1	s__Vibrio harveyi	80.1874	450	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:03,292] [INFO] GTDB search result was written to GCF_024582835.1_ASM2458283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:03,293] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:03,298] [INFO] DFAST_QC result json was written to GCF_024582835.1_ASM2458283v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:03,298] [INFO] DFAST_QC completed!
[2024-01-24 11:28:03,298] [INFO] Total running time: 0h1m25s