[2024-01-24 11:52:04,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg6242ecfd-a9ac-405d-8db8-bbc921824d02/dqc_reference
[2024-01-24 11:52:05,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,892] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg92c2f714-d55d-450a-b699-1834ae834f53/GCF_025195085.2_ASM2519508v2_genomic.fna.gz | prodigal -d GCF_025195085.2_ASM2519508v2_genomic.fna/cds.fna -a GCF_025195085.2_ASM2519508v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:16,052] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:16,053] [INFO] Task started: HMMsearch
[2024-01-24 11:52:16,053] [INFO] Running command: hmmsearch --tblout GCF_025195085.2_ASM2519508v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6242ecfd-a9ac-405d-8db8-bbc921824d02/dqc_reference/reference_markers.hmm GCF_025195085.2_ASM2519508v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:16,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:16,337] [INFO] Found 6/6 markers.
[2024-01-24 11:52:16,378] [INFO] Query marker FASTA was written to GCF_025195085.2_ASM2519508v2_genomic.fna/markers.fasta
[2024-01-24 11:52:16,379] [INFO] Task started: Blastn
[2024-01-24 11:52:16,379] [INFO] Running command: blastn -query GCF_025195085.2_ASM2519508v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6242ecfd-a9ac-405d-8db8-bbc921824d02/dqc_reference/reference_markers.fasta -out GCF_025195085.2_ASM2519508v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:17,148] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:17,153] [INFO] Selected 26 target genomes.
[2024-01-24 11:52:17,154] [INFO] Target genome list was writen to GCF_025195085.2_ASM2519508v2_genomic.fna/target_genomes.txt
[2024-01-24 11:52:17,211] [INFO] Task started: fastANI
[2024-01-24 11:52:17,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c2f714-d55d-450a-b699-1834ae834f53/GCF_025195085.2_ASM2519508v2_genomic.fna.gz --refList GCF_025195085.2_ASM2519508v2_genomic.fna/target_genomes.txt --output GCF_025195085.2_ASM2519508v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:38,132] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:38,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6242ecfd-a9ac-405d-8db8-bbc921824d02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:38,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6242ecfd-a9ac-405d-8db8-bbc921824d02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:38,164] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:38,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:38,165] [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 rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	81.0453	586	1431	95	below_threshold
Vibrio ponticus	strain=DSM 16217	GCA_009938225.1	265668	265668	type	True	80.9792	575	1431	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	80.9444	517	1431	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	80.9372	525	1431	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	80.9263	557	1431	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	80.824	538	1431	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	80.7952	531	1431	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	80.694	513	1431	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	80.6695	547	1431	95	below_threshold
Vibrio harveyi	strain=FDAARGOS_109	GCA_001471575.2	669	669	type	True	80.6344	494	1431	95	below_threshold
Vibrio maerlii	strain=G62	GCA_003415655.1	2231648	2231648	type	True	80.6014	369	1431	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	80.5929	523	1431	95	below_threshold
Vibrio harveyi	strain=NCTC12970	GCA_900460165.1	669	669	type	True	80.5668	493	1431	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	80.5555	540	1431	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	80.5033	557	1431	95	below_threshold
Vibrio harveyi	strain=NBRC 15634	GCA_001591145.1	669	669	type	True	80.4733	475	1431	95	below_threshold
Vibrio harveyi	strain=ATCC 14126	GCA_001263135.1	669	669	type	True	80.4515	484	1431	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	80.3795	445	1431	95	below_threshold
Vibrio campbellii	strain=CAIM 519	GCA_000334195.1	680	680	type	True	80.3536	474	1431	95	below_threshold
Vibrio nereis	strain=NBRC 15637	GCA_001591105.1	693	693	type	True	80.3523	459	1431	95	below_threshold
Vibrio nereis	strain=DSM 19584	GCA_001274805.1	693	693	type	True	80.2777	462	1431	95	below_threshold
Vibrio pelagius	strain=ATCC 25916	GCA_024347575.1	28169	28169	type	True	80.2554	425	1431	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	80.1444	428	1431	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	79.9631	445	1431	95	below_threshold
Vibrio sinensis	strain=BEI233	GCA_003605645.1	2302434	2302434	type	True	79.7771	475	1431	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	79.7666	443	1431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:38,167] [INFO] DFAST Taxonomy check result was written to GCF_025195085.2_ASM2519508v2_genomic.fna/tc_result.tsv
[2024-01-24 11:52:38,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:38,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:38,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6242ecfd-a9ac-405d-8db8-bbc921824d02/dqc_reference/checkm_data
[2024-01-24 11:52:38,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:38,208] [INFO] Task started: CheckM
[2024-01-24 11:52:38,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025195085.2_ASM2519508v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025195085.2_ASM2519508v2_genomic.fna/checkm_input GCF_025195085.2_ASM2519508v2_genomic.fna/checkm_result
[2024-01-24 11:53:12,761] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:12,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:12,783] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:12,784] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:12,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025195085.2_ASM2519508v2_genomic.fna/markers.fasta)
[2024-01-24 11:53:12,784] [INFO] Task started: Blastn
[2024-01-24 11:53:12,784] [INFO] Running command: blastn -query GCF_025195085.2_ASM2519508v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6242ecfd-a9ac-405d-8db8-bbc921824d02/dqc_reference/reference_markers_gtdb.fasta -out GCF_025195085.2_ASM2519508v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:13,807] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:13,811] [INFO] Selected 24 target genomes.
[2024-01-24 11:53:13,812] [INFO] Target genome list was writen to GCF_025195085.2_ASM2519508v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:13,828] [INFO] Task started: fastANI
[2024-01-24 11:53:13,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg92c2f714-d55d-450a-b699-1834ae834f53/GCF_025195085.2_ASM2519508v2_genomic.fna.gz --refList GCF_025195085.2_ASM2519508v2_genomic.fna/target_genomes_gtdb.txt --output GCF_025195085.2_ASM2519508v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:34,045] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:34,069] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:34,069] [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_003350325.1	s__Vibrio rhodolitus	81.0525	585	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.24	97.24	0.91	0.91	2	-
GCF_009938225.1	s__Vibrio ponticus	80.9858	574	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.69	97.39	0.92	0.85	3	-
GCF_000176235.1	s__Vibrio orientalis	80.9372	525	1431	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	80.9263	557	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_013114545.1	s__Vibrio sp013114545	80.8897	507	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004551525.1	s__Vibrio ouci	80.8275	534	1431	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	80.8215	537	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811315.1	s__Vibrio atypicus	80.8203	526	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_000772105.1	s__Vibrio tubiashii	80.8071	530	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_009938165.1	s__Vibrio taketomensis	80.7571	531	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_000189255.1	s__Vibrio brasiliensis	80.6604	490	1431	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	80.6487	500	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_015278125.1	s__Vibrio sp015278125	80.6252	581	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003415655.1	s__Vibrio maerlii	80.6222	367	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274785.1	s__Vibrio hepatarius	80.6134	494	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_011806575.1	s__Vibrio hepatarius_A	80.581	488	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_001695575.1	s__Vibrio europaeus	80.5622	539	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_000695685.1	s__Vibrio fortis	80.5591	431	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.41	96.21	0.90	0.88	4	-
GCF_002741985.1	s__Vibrio rotiferianus	80.5526	490	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_000189275.1	s__Vibrio sinaloensis_B	80.5178	484	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591145.1	s__Vibrio harveyi	80.4645	475	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_001591105.1	s__Vibrio nereis	80.3627	457	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000272045.2	s__Vibrio crassostreae_C	79.9043	457	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_000171815.1	s__Vibrio sp000171815	79.6711	357	1431	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 11:53:34,071] [INFO] GTDB search result was written to GCF_025195085.2_ASM2519508v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:34,072] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:34,077] [INFO] DFAST_QC result json was written to GCF_025195085.2_ASM2519508v2_genomic.fna/dqc_result.json
[2024-01-24 11:53:34,077] [INFO] DFAST_QC completed!
[2024-01-24 11:53:34,077] [INFO] Total running time: 0h1m29s