[2024-01-25 20:25:35,571] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:25:35,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:25:35,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bc40088-55bb-409c-a5bd-9a3930d027dc/dqc_reference
[2024-01-25 20:25:36,770] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:25:36,771] [INFO] Task started: Prodigal
[2024-01-25 20:25:36,771] [INFO] Running command: gunzip -c /var/lib/cwl/stgb529590d-e309-4a72-bbb3-0d3cc97e093b/GCF_030409945.1_ASM3040994v1_genomic.fna.gz | prodigal -d GCF_030409945.1_ASM3040994v1_genomic.fna/cds.fna -a GCF_030409945.1_ASM3040994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:25:47,567] [INFO] Task succeeded: Prodigal
[2024-01-25 20:25:47,567] [INFO] Task started: HMMsearch
[2024-01-25 20:25:47,568] [INFO] Running command: hmmsearch --tblout GCF_030409945.1_ASM3040994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bc40088-55bb-409c-a5bd-9a3930d027dc/dqc_reference/reference_markers.hmm GCF_030409945.1_ASM3040994v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:25:47,816] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:25:47,817] [INFO] Found 6/6 markers.
[2024-01-25 20:25:47,860] [INFO] Query marker FASTA was written to GCF_030409945.1_ASM3040994v1_genomic.fna/markers.fasta
[2024-01-25 20:25:47,860] [INFO] Task started: Blastn
[2024-01-25 20:25:47,860] [INFO] Running command: blastn -query GCF_030409945.1_ASM3040994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bc40088-55bb-409c-a5bd-9a3930d027dc/dqc_reference/reference_markers.fasta -out GCF_030409945.1_ASM3040994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:48,614] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:48,617] [INFO] Selected 31 target genomes.
[2024-01-25 20:25:48,617] [INFO] Target genome list was writen to GCF_030409945.1_ASM3040994v1_genomic.fna/target_genomes.txt
[2024-01-25 20:25:48,676] [INFO] Task started: fastANI
[2024-01-25 20:25:48,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgb529590d-e309-4a72-bbb3-0d3cc97e093b/GCF_030409945.1_ASM3040994v1_genomic.fna.gz --refList GCF_030409945.1_ASM3040994v1_genomic.fna/target_genomes.txt --output GCF_030409945.1_ASM3040994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:12,909] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:12,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bc40088-55bb-409c-a5bd-9a3930d027dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:12,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bc40088-55bb-409c-a5bd-9a3930d027dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:12,928] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:26:12,928] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:26:12,928] [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 splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.7585	374	1709	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	79.6432	328	1709	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.6304	335	1709	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	79.6289	331	1709	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	79.6239	378	1709	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	79.5918	377	1709	95	below_threshold
Vibrio toranzoniae	strain=Vb 10.8	GCA_001541335.1	1194427	1194427	type	True	79.5843	334	1709	95	below_threshold
Vibrio celticus	strain=Rd 8.15	GCA_002156525.1	446372	446372	type	True	79.5729	356	1709	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	79.5481	351	1709	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	79.5373	368	1709	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	79.5246	375	1709	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	79.4842	197	1709	95	below_threshold
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	79.4791	367	1709	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	79.4641	375	1709	95	below_threshold
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	79.4362	201	1709	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.3684	342	1709	95	below_threshold
Vibrio inusitatus	strain=NBRC 102082	GCA_006538525.1	413402	413402	type	True	79.329	195	1709	95	below_threshold
Vibrio penaeicida	strain=CAIM 285	GCA_003970425.1	104609	104609	type	True	79.204	321	1709	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	79.1526	347	1709	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	79.0855	277	1709	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	79.0854	276	1709	95	below_threshold
Vibrio nigripulchritudo	strain=ATCC 27043	GCA_000222685.2	28173	28173	type	True	79.0363	323	1709	95	below_threshold
Vibrio sinensis	strain=BEI233	GCA_003605645.1	2302434	2302434	type	True	79.0066	285	1709	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	78.9686	298	1709	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	78.8137	293	1709	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	78.8002	291	1709	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.7964	231	1709	95	below_threshold
Aliivibrio fischeri	strain=ATCC 7744	GCA_016464335.1	668	668	suspected-type	True	78.6367	226	1709	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	78.5939	291	1709	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	78.5656	299	1709	95	below_threshold
Vibrio aestuarianus	strain=LMG 7909	GCA_012395185.1	28171	28171	type	True	78.5326	309	1709	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:12,930] [INFO] DFAST Taxonomy check result was written to GCF_030409945.1_ASM3040994v1_genomic.fna/tc_result.tsv
[2024-01-25 20:26:12,930] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:12,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:12,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bc40088-55bb-409c-a5bd-9a3930d027dc/dqc_reference/checkm_data
[2024-01-25 20:26:12,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:12,985] [INFO] Task started: CheckM
[2024-01-25 20:26:12,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409945.1_ASM3040994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409945.1_ASM3040994v1_genomic.fna/checkm_input GCF_030409945.1_ASM3040994v1_genomic.fna/checkm_result
[2024-01-25 20:26:47,590] [INFO] Task succeeded: CheckM
[2024-01-25 20:26:47,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:26:47,609] [INFO] ===== Completeness check finished =====
[2024-01-25 20:26:47,610] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:26:47,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409945.1_ASM3040994v1_genomic.fna/markers.fasta)
[2024-01-25 20:26:47,610] [INFO] Task started: Blastn
[2024-01-25 20:26:47,610] [INFO] Running command: blastn -query GCF_030409945.1_ASM3040994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bc40088-55bb-409c-a5bd-9a3930d027dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409945.1_ASM3040994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:48,782] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:48,784] [INFO] Selected 23 target genomes.
[2024-01-25 20:26:48,784] [INFO] Target genome list was writen to GCF_030409945.1_ASM3040994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:26:48,817] [INFO] Task started: fastANI
[2024-01-25 20:26:48,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgb529590d-e309-4a72-bbb3-0d3cc97e093b/GCF_030409945.1_ASM3040994v1_genomic.fna.gz --refList GCF_030409945.1_ASM3040994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409945.1_ASM3040994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:27:08,118] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:08,131] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:27:08,132] [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_900233005.1	s__Vibrio tapetis	89.5027	1344	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272045.2	s__Vibrio crassostreae_C	79.6093	383	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_002156525.1	s__Vibrio celticus	79.5832	356	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_014879975.1	s__Vibrio bathopelagicus	79.4555	366	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	79.4379	330	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_000272145.2	s__Vibrio sp000272145	79.2913	321	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.26	98.15	0.92	0.92	4	-
GCF_002877365.1	s__Vibrio sp002877365	79.207	287	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970425.1	s__Vibrio penaeicida	79.2048	324	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	-
GCF_007858795.1	s__Vibrio sp007858795	79.1992	368	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002873395.1	s__Vibrio sp002873395	79.1961	286	1709	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	79.174	308	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272105.2	s__Vibrio splendidus_I	79.1612	369	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933855.1	s__Vibrio penaeicida_A	79.0884	349	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222605.1	s__Vibrio ichthyoenteri	79.0727	277	1709	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	79.0226	324	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.90	96.77	0.92	0.87	18	-
GCF_003605645.1	s__Vibrio sinensis	79.0011	284	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874155.1	s__Vibrio sp001874155	78.9899	222	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163755.1	s__Vibrio campbellii	78.9489	311	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_001695575.1	s__Vibrio europaeus	78.9386	300	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000772105.1	s__Vibrio tubiashii	78.9152	302	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_000176235.1	s__Vibrio orientalis	78.8734	296	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000222585.1	s__Vibrio scophthalmi	78.623	291	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_900312675.1	s__Aliivibrio sp900312675	78.5668	256	1709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Aliivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:27:08,133] [INFO] GTDB search result was written to GCF_030409945.1_ASM3040994v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:27:08,134] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:27:08,139] [INFO] DFAST_QC result json was written to GCF_030409945.1_ASM3040994v1_genomic.fna/dqc_result.json
[2024-01-25 20:27:08,139] [INFO] DFAST_QC completed!
[2024-01-25 20:27:08,139] [INFO] Total running time: 0h1m33s