[2024-01-24 11:43:42,330] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,332] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg75ca0a96-9b37-41cf-ae55-296122494317/dqc_reference
[2024-01-24 11:43:43,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,637] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b8ecf6f-f649-4312-85b3-12757a1df8dd/GCF_015686695.1_ASM1568669v1_genomic.fna.gz | prodigal -d GCF_015686695.1_ASM1568669v1_genomic.fna/cds.fna -a GCF_015686695.1_ASM1568669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:56,757] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:56,757] [INFO] Task started: HMMsearch
[2024-01-24 11:43:56,758] [INFO] Running command: hmmsearch --tblout GCF_015686695.1_ASM1568669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75ca0a96-9b37-41cf-ae55-296122494317/dqc_reference/reference_markers.hmm GCF_015686695.1_ASM1568669v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:57,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:57,213] [INFO] Found 6/6 markers.
[2024-01-24 11:43:57,259] [INFO] Query marker FASTA was written to GCF_015686695.1_ASM1568669v1_genomic.fna/markers.fasta
[2024-01-24 11:43:57,260] [INFO] Task started: Blastn
[2024-01-24 11:43:57,260] [INFO] Running command: blastn -query GCF_015686695.1_ASM1568669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75ca0a96-9b37-41cf-ae55-296122494317/dqc_reference/reference_markers.fasta -out GCF_015686695.1_ASM1568669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:58,108] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:58,111] [INFO] Selected 24 target genomes.
[2024-01-24 11:43:58,111] [INFO] Target genome list was writen to GCF_015686695.1_ASM1568669v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:58,122] [INFO] Task started: fastANI
[2024-01-24 11:43:58,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b8ecf6f-f649-4312-85b3-12757a1df8dd/GCF_015686695.1_ASM1568669v1_genomic.fna.gz --refList GCF_015686695.1_ASM1568669v1_genomic.fna/target_genomes.txt --output GCF_015686695.1_ASM1568669v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:26,064] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:26,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75ca0a96-9b37-41cf-ae55-296122494317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:26,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75ca0a96-9b37-41cf-ae55-296122494317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:26,084] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:26,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:26,084] [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 nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	100.0	1816	1822	95	conclusive
Vibrio tritonius	strain=JCM 16456	GCA_001547935.1	1435069	1435069	type	True	80.9733	710	1822	95	below_threshold
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	80.8498	721	1822	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	80.2158	199	1822	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	80.0569	331	1822	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	80.0479	249	1822	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	80.0057	252	1822	95	below_threshold
Vibrio palustris	strain=CECT 9027	GCA_024346995.1	1918946	1918946	type	True	79.9427	354	1822	95	below_threshold
Vibrio furnissii	strain=FDAARGOS_777	GCA_006364355.1	29494	29494	type	True	79.9094	337	1822	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	79.7987	268	1822	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_002906655.1	1534743	1534743	type	True	79.7174	276	1822	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.5883	254	1822	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.4674	241	1822	95	below_threshold
Vibrio hippocampi	strain=CECT 8226	GCA_921292975.1	654686	654686	type	True	79.4661	199	1822	95	below_threshold
Vibrio palustris	strain=CECT 9027	GCA_900162645.1	1918946	1918946	type	True	79.3966	342	1822	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	79.3938	320	1822	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	79.3682	213	1822	95	below_threshold
Vibrio gallaecicus	strain=CECT 7244	GCA_024347495.1	552386	552386	type	True	79.1407	256	1822	95	below_threshold
Vibrio thalassae	strain=CECT8203	GCA_900089835.1	1243014	1243014	type	True	78.9993	220	1822	95	below_threshold
Vibrio alginolyticus	strain=NBRC 15630	GCA_000467145.1	663	663	type	True	78.9964	236	1822	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	78.9914	252	1822	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	78.812	254	1822	95	below_threshold
Vibrio variabilis	strain=CAIM 1454	GCA_003263785.1	990271	990271	type	True	78.7604	217	1822	95	below_threshold
Vibrio aestuarianus subsp. cardii	strain=12/122 3T3	GCA_011090275.1	2807650	28171	type	True	78.7171	306	1822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:26,086] [INFO] DFAST Taxonomy check result was written to GCF_015686695.1_ASM1568669v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:26,086] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:26,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:26,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75ca0a96-9b37-41cf-ae55-296122494317/dqc_reference/checkm_data
[2024-01-24 11:44:26,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:26,143] [INFO] Task started: CheckM
[2024-01-24 11:44:26,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015686695.1_ASM1568669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015686695.1_ASM1568669v1_genomic.fna/checkm_input GCF_015686695.1_ASM1568669v1_genomic.fna/checkm_result
[2024-01-24 11:45:08,879] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:08,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:08,905] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:08,905] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:08,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015686695.1_ASM1568669v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:08,906] [INFO] Task started: Blastn
[2024-01-24 11:45:08,906] [INFO] Running command: blastn -query GCF_015686695.1_ASM1568669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75ca0a96-9b37-41cf-ae55-296122494317/dqc_reference/reference_markers_gtdb.fasta -out GCF_015686695.1_ASM1568669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:10,191] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:10,195] [INFO] Selected 22 target genomes.
[2024-01-24 11:45:10,195] [INFO] Target genome list was writen to GCF_015686695.1_ASM1568669v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:10,225] [INFO] Task started: fastANI
[2024-01-24 11:45:10,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b8ecf6f-f649-4312-85b3-12757a1df8dd/GCF_015686695.1_ASM1568669v1_genomic.fna.gz --refList GCF_015686695.1_ASM1568669v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015686695.1_ASM1568669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:31,708] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:31,732] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:31,732] [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_015686695.1	s__Vibrio nitrifigilis	100.0	1816	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.79	98.79	0.95	0.95	2	conclusive
GCF_001547935.1	s__Vibrio tritonius	80.955	709	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003716875.1	s__Vibrio zhugei	80.2365	333	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460245.1	s__Vibrio fluvialis	80.2241	328	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_002163755.1	s__Vibrio campbellii	80.1504	270	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_000772105.1	s__Vibrio tubiashii	79.8634	269	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_000354175.2	s__Vibrio alginolyticus	79.8305	247	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.30	0.93	0.90	169	-
GCF_002906655.1	s__Vibrio hyugaensis	79.7252	276	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_001695575.1	s__Vibrio europaeus	79.5741	254	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.44	98.30	0.92	0.91	4	-
GCF_900162645.1	s__Vibrio palustris	79.4135	341	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176175.1	s__Vibrio furnissii	79.3773	321	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_002741985.1	s__Vibrio rotiferianus	79.1813	246	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_001591105.1	s__Vibrio nereis	79.0769	238	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000740015.1	s__Vibrio diazotrophicus	79.0386	324	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_000189275.1	s__Vibrio sinaloensis_B	79.0077	226	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089835.1	s__Vibrio thalassae	78.9793	222	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.8081	N/A	N/A	N/A	N/A	1	-
GCF_900107935.1	s__Vibrio hangzhouensis	78.9488	182	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000755425.1	s__Vibrio maritimus_A	78.8366	218	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003263785.1	s__Vibrio variabilis	78.7604	217	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400365.1	s__Vibrio jasicida	78.6414	270	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_002933855.1	s__Vibrio penaeicida_A	78.6357	201	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272145.2	s__Vibrio sp000272145	78.4805	214	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.26	98.15	0.92	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:31,734] [INFO] GTDB search result was written to GCF_015686695.1_ASM1568669v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:31,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:31,742] [INFO] DFAST_QC result json was written to GCF_015686695.1_ASM1568669v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:31,743] [INFO] DFAST_QC completed!
[2024-01-24 11:45:31,743] [INFO] Total running time: 0h1m49s