[2024-01-25 18:49:35,728] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:35,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:35,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg05afefba-1a40-4c98-9dd8-e982630dd476/dqc_reference
[2024-01-25 18:49:36,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:36,869] [INFO] Task started: Prodigal
[2024-01-25 18:49:36,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb5c758-56bf-43c5-af5b-8871edfb3953/GCF_019977755.1_ASM1997775v1_genomic.fna.gz | prodigal -d GCF_019977755.1_ASM1997775v1_genomic.fna/cds.fna -a GCF_019977755.1_ASM1997775v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:52,341] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:52,342] [INFO] Task started: HMMsearch
[2024-01-25 18:49:52,342] [INFO] Running command: hmmsearch --tblout GCF_019977755.1_ASM1997775v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05afefba-1a40-4c98-9dd8-e982630dd476/dqc_reference/reference_markers.hmm GCF_019977755.1_ASM1997775v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:52,680] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:52,681] [INFO] Found 6/6 markers.
[2024-01-25 18:49:52,734] [INFO] Query marker FASTA was written to GCF_019977755.1_ASM1997775v1_genomic.fna/markers.fasta
[2024-01-25 18:49:52,734] [INFO] Task started: Blastn
[2024-01-25 18:49:52,734] [INFO] Running command: blastn -query GCF_019977755.1_ASM1997775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05afefba-1a40-4c98-9dd8-e982630dd476/dqc_reference/reference_markers.fasta -out GCF_019977755.1_ASM1997775v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:53,516] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:53,520] [INFO] Selected 21 target genomes.
[2024-01-25 18:49:53,521] [INFO] Target genome list was writen to GCF_019977755.1_ASM1997775v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:53,587] [INFO] Task started: fastANI
[2024-01-25 18:49:53,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb5c758-56bf-43c5-af5b-8871edfb3953/GCF_019977755.1_ASM1997775v1_genomic.fna.gz --refList GCF_019977755.1_ASM1997775v1_genomic.fna/target_genomes.txt --output GCF_019977755.1_ASM1997775v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:15,307] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:15,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05afefba-1a40-4c98-9dd8-e982630dd476/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:15,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05afefba-1a40-4c98-9dd8-e982630dd476/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:15,321] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:50:15,321] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:15,321] [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 penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	100.0	2258	2260	95	conclusive
Vibrio penaeicida	strain=CAIM 285	GCA_003970425.1	104609	104609	type	True	99.8236	1878	2260	95	conclusive
Vibrio nigripulchritudo	strain=ATCC 27043	GCA_000222685.2	28173	28173	type	True	81.8091	964	2260	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	80.2861	318	2260	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.2498	293	2260	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	80.22	296	2260	95	below_threshold
Vibrio parahaemolyticus	strain=NCTC10903	GCA_900460535.1	670	670	type	True	80.1905	303	2260	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	80.1578	313	2260	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	80.1198	324	2260	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	79.9445	302	2260	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.8575	324	2260	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.78	290	2260	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.6424	303	2260	95	below_threshold
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	79.6274	284	2260	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.4085	303	2260	95	below_threshold
Vibrio parahaemolyticus	strain=ATCC 17802	GCA_001011015.1	670	670	type	True	79.3688	285	2260	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	79.174	283	2260	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	79.0991	272	2260	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	78.9866	248	2260	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	78.8406	258	2260	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	78.7952	267	2260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:15,322] [INFO] DFAST Taxonomy check result was written to GCF_019977755.1_ASM1997775v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:15,323] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:15,323] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:15,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05afefba-1a40-4c98-9dd8-e982630dd476/dqc_reference/checkm_data
[2024-01-25 18:50:15,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:15,387] [INFO] Task started: CheckM
[2024-01-25 18:50:15,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019977755.1_ASM1997775v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019977755.1_ASM1997775v1_genomic.fna/checkm_input GCF_019977755.1_ASM1997775v1_genomic.fna/checkm_result
[2024-01-25 18:51:05,089] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:05,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:05,109] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:05,110] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:05,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019977755.1_ASM1997775v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:05,110] [INFO] Task started: Blastn
[2024-01-25 18:51:05,110] [INFO] Running command: blastn -query GCF_019977755.1_ASM1997775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05afefba-1a40-4c98-9dd8-e982630dd476/dqc_reference/reference_markers_gtdb.fasta -out GCF_019977755.1_ASM1997775v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:06,329] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:06,332] [INFO] Selected 14 target genomes.
[2024-01-25 18:51:06,332] [INFO] Target genome list was writen to GCF_019977755.1_ASM1997775v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:06,343] [INFO] Task started: fastANI
[2024-01-25 18:51:06,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb5c758-56bf-43c5-af5b-8871edfb3953/GCF_019977755.1_ASM1997775v1_genomic.fna.gz --refList GCF_019977755.1_ASM1997775v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019977755.1_ASM1997775v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:24,720] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:24,729] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:24,729] [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_003970425.1	s__Vibrio penaeicida	99.8213	1879	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	conclusive
GCF_002933855.1	s__Vibrio penaeicida_A	92.6081	1816	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694455.1	s__Vibrio sp014694455	85.4618	1422	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222685.1	s__Vibrio nigripulchritudo	81.8314	958	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.90	96.77	0.92	0.87	18	-
GCF_000772105.1	s__Vibrio tubiashii	80.3342	315	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_900233005.1	s__Vibrio tapetis	79.4911	362	2260	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	79.4575	274	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970385.1	s__Vibrio aquaticus	79.4436	302	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808535.1	s__Vibrio sinaloensis	79.4234	279	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_009938165.1	s__Vibrio taketomensis	79.3116	268	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_009811315.1	s__Vibrio atypicus	79.1114	316	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000189255.1	s__Vibrio brasiliensis	79.0838	269	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222585.1	s__Vibrio scophthalmi	79.0042	247	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCA_018223135.1	s__Vibrio sp018223135	78.8758	264	2260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:24,731] [INFO] GTDB search result was written to GCF_019977755.1_ASM1997775v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:24,731] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:24,734] [INFO] DFAST_QC result json was written to GCF_019977755.1_ASM1997775v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:24,734] [INFO] DFAST_QC completed!
[2024-01-25 18:51:24,734] [INFO] Total running time: 0h1m49s