[2024-01-24 13:31:12,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg88055c52-a567-4265-8aca-ac5e4ab33bad/dqc_reference
[2024-01-24 13:31:13,227] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,228] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,228] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbdcce44-146e-48e2-bc8b-a6047ef621c8/GCF_012641465.1_ASM1264146v1_genomic.fna.gz | prodigal -d GCF_012641465.1_ASM1264146v1_genomic.fna/cds.fna -a GCF_012641465.1_ASM1264146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:24,404] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:24,404] [INFO] Task started: HMMsearch
[2024-01-24 13:31:24,404] [INFO] Running command: hmmsearch --tblout GCF_012641465.1_ASM1264146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88055c52-a567-4265-8aca-ac5e4ab33bad/dqc_reference/reference_markers.hmm GCF_012641465.1_ASM1264146v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:24,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:24,640] [INFO] Found 6/6 markers.
[2024-01-24 13:31:24,676] [INFO] Query marker FASTA was written to GCF_012641465.1_ASM1264146v1_genomic.fna/markers.fasta
[2024-01-24 13:31:24,676] [INFO] Task started: Blastn
[2024-01-24 13:31:24,676] [INFO] Running command: blastn -query GCF_012641465.1_ASM1264146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88055c52-a567-4265-8aca-ac5e4ab33bad/dqc_reference/reference_markers.fasta -out GCF_012641465.1_ASM1264146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:25,459] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:25,463] [INFO] Selected 23 target genomes.
[2024-01-24 13:31:25,463] [INFO] Target genome list was writen to GCF_012641465.1_ASM1264146v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:25,471] [INFO] Task started: fastANI
[2024-01-24 13:31:25,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbdcce44-146e-48e2-bc8b-a6047ef621c8/GCF_012641465.1_ASM1264146v1_genomic.fna.gz --refList GCF_012641465.1_ASM1264146v1_genomic.fna/target_genomes.txt --output GCF_012641465.1_ASM1264146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:44,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:44,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88055c52-a567-4265-8aca-ac5e4ab33bad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:44,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88055c52-a567-4265-8aca-ac5e4ab33bad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:44,645] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:44,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:44,646] [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 agarilyticus	strain=SM6	GCA_012641465.1	2726741	2726741	type	True	100.0	1418	1420	95	conclusive
Vibrio rhodolitus	strain=G98	GCA_003350325.1	2231649	2231649	type	True	79.2299	250	1420	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.1742	242	1420	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.1575	248	1420	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	79.153	219	1420	95	below_threshold
Vibrio owensii	strain=DY05	GCA_000817815.1	696485	696485	type	True	79.053	256	1420	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.9981	252	1420	95	below_threshold
Vibrio azureus	strain=LC2-005	GCA_002849855.1	512649	512649	type	True	78.9503	218	1420	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	78.9111	216	1420	95	below_threshold
Vibrio rotiferianus	strain=CAIM 577	GCA_002741985.1	190895	190895	type	True	78.901	275	1420	95	below_threshold
Vibrio azureus	strain=NBRC 104587	GCA_000467165.1	512649	512649	type	True	78.8586	206	1420	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	78.8501	219	1420	95	below_threshold
Vibrio scophthalmi	strain=LMG 19158	GCA_000222585.2	45658	45658	type	True	78.8294	247	1420	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	78.7873	271	1420	95	below_threshold
Vibrio azureus	strain=NBRC 104587	GCA_000400265.1	512649	512649	type	True	78.7281	205	1420	95	below_threshold
Vibrio fluvialis	strain=NBRC 103150	GCA_001598835.1	676	676	type	True	78.7214	216	1420	95	below_threshold
Vibrio xiamenensis	strain=CGMCC 1.10228	GCA_900100015.1	861298	861298	type	True	78.7092	240	1420	95	below_threshold
Vibrio mimicus	strain=NCTC11435	GCA_900460385.1	674	674	type	True	78.5826	222	1420	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.5292	193	1420	95	below_threshold
Vibrio mimicus	strain=CAIM 602	GCA_000338875.1	674	674	type	True	78.4842	225	1420	95	below_threshold
Thaumasiovibrio occultus	strain=C4II189	GCA_019703815.1	1891184	1891184	type	True	78.3911	138	1420	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	78.2969	237	1420	95	below_threshold
Vibrio furnissii	strain=CIP 102972	GCA_000176175.1	29494	29494	type	True	78.262	251	1420	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:44,647] [INFO] DFAST Taxonomy check result was written to GCF_012641465.1_ASM1264146v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:44,648] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:44,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:44,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88055c52-a567-4265-8aca-ac5e4ab33bad/dqc_reference/checkm_data
[2024-01-24 13:31:44,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:44,691] [INFO] Task started: CheckM
[2024-01-24 13:31:44,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012641465.1_ASM1264146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012641465.1_ASM1264146v1_genomic.fna/checkm_input GCF_012641465.1_ASM1264146v1_genomic.fna/checkm_result
[2024-01-24 13:32:22,764] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:22,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:22,788] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:22,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:22,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012641465.1_ASM1264146v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:22,789] [INFO] Task started: Blastn
[2024-01-24 13:32:22,789] [INFO] Running command: blastn -query GCF_012641465.1_ASM1264146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88055c52-a567-4265-8aca-ac5e4ab33bad/dqc_reference/reference_markers_gtdb.fasta -out GCF_012641465.1_ASM1264146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:24,097] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:24,100] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:24,101] [INFO] Target genome list was writen to GCF_012641465.1_ASM1264146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:24,123] [INFO] Task started: fastANI
[2024-01-24 13:32:24,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbdcce44-146e-48e2-bc8b-a6047ef621c8/GCF_012641465.1_ASM1264146v1_genomic.fna.gz --refList GCF_012641465.1_ASM1264146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012641465.1_ASM1264146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:45,177] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:45,196] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:45,196] [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_012641465.1	s__Vibrio agarilyticus	100.0	1418	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009938165.1	s__Vibrio taketomensis	79.6309	237	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_002163755.1	s__Vibrio campbellii	79.433	250	1420	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	79.2655	234	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009938205.1	s__Vibrio panuliri	79.1913	241	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.52	98.57	0.98	0.94	4	-
GCF_001274785.1	s__Vibrio hepatarius	79.1856	224	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_000817815.1	s__Vibrio owensii	79.0607	256	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.72	96.06	0.85	0.79	29	-
GCF_000967545.1	s__Vibrio galatheae	79.0056	207	1420	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	78.9992	252	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.80	98.53	0.95	0.89	41	-
GCF_002741985.1	s__Vibrio rotiferianus	78.9311	274	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.35	95.73	0.89	0.85	14	-
GCF_905175385.1	s__Vibrio sp903986855	78.9237	248	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.95	0.95	0.92	4	-
GCF_002849855.1	s__Vibrio azureus	78.9051	221	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900460245.1	s__Vibrio fluvialis	78.8919	216	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_002906655.1	s__Vibrio hyugaensis	78.8573	277	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.28	97.73	0.94	0.90	6	-
GCF_000222585.1	s__Vibrio scophthalmi	78.8466	246	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.31	96.70	0.87	0.84	5	-
GCF_000400365.1	s__Vibrio jasicida	78.8229	266	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCA_015767675.1	s__Vibrio sp000960595	78.7852	275	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.64	97.38	0.94	0.90	8	-
GCF_019226825.1	s__Vibrio sp004804295	78.7646	191	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.23	99.23	0.93	0.93	2	-
GCF_900100015.1	s__Vibrio xiamenensis	78.6922	241	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338875.1	s__Vibrio mimicus	78.5006	224	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.81	0.94	0.91	26	-
GCF_009665255.1	s__Vibrio metoecus_B	78.4783	215	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.11	98.11	0.94	0.94	2	-
GCF_019048845.1	s__Vibrio sp000176715	78.4246	221	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.20	96.20	0.92	0.92	2	-
GCF_011306175.1	s__Vibrio sp011306175	78.3338	215	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157795.1	s__Thaumasiovibrio occultus	78.3225	139	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Thaumasiovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:45,198] [INFO] GTDB search result was written to GCF_012641465.1_ASM1264146v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:45,198] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:45,203] [INFO] DFAST_QC result json was written to GCF_012641465.1_ASM1264146v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:45,203] [INFO] DFAST_QC completed!
[2024-01-24 13:32:45,204] [INFO] Total running time: 0h1m33s