[2024-01-24 14:38:47,002] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:47,004] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:47,004] [INFO] DQC Reference Directory: /var/lib/cwl/stg4189c0d0-98dc-47de-823c-e46223784fe8/dqc_reference
[2024-01-24 14:38:48,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,256] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg19a6f1e4-327b-4905-bb58-796f149e9621/GCF_013074385.2_ASM1307438v2_genomic.fna.gz | prodigal -d GCF_013074385.2_ASM1307438v2_genomic.fna/cds.fna -a GCF_013074385.2_ASM1307438v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:59,530] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:59,530] [INFO] Task started: HMMsearch
[2024-01-24 14:38:59,530] [INFO] Running command: hmmsearch --tblout GCF_013074385.2_ASM1307438v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4189c0d0-98dc-47de-823c-e46223784fe8/dqc_reference/reference_markers.hmm GCF_013074385.2_ASM1307438v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:59,846] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:59,848] [INFO] Found 6/6 markers.
[2024-01-24 14:38:59,889] [INFO] Query marker FASTA was written to GCF_013074385.2_ASM1307438v2_genomic.fna/markers.fasta
[2024-01-24 14:38:59,890] [INFO] Task started: Blastn
[2024-01-24 14:38:59,890] [INFO] Running command: blastn -query GCF_013074385.2_ASM1307438v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4189c0d0-98dc-47de-823c-e46223784fe8/dqc_reference/reference_markers.fasta -out GCF_013074385.2_ASM1307438v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:00,646] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:00,649] [INFO] Selected 24 target genomes.
[2024-01-24 14:39:00,650] [INFO] Target genome list was writen to GCF_013074385.2_ASM1307438v2_genomic.fna/target_genomes.txt
[2024-01-24 14:39:00,661] [INFO] Task started: fastANI
[2024-01-24 14:39:00,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg19a6f1e4-327b-4905-bb58-796f149e9621/GCF_013074385.2_ASM1307438v2_genomic.fna.gz --refList GCF_013074385.2_ASM1307438v2_genomic.fna/target_genomes.txt --output GCF_013074385.2_ASM1307438v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:18,510] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:18,511] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4189c0d0-98dc-47de-823c-e46223784fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:18,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4189c0d0-98dc-47de-823c-e46223784fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:18,528] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:18,528] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:18,529] [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 ostreicida	strain=PP-203	GCA_013074385.2	526588	526588	type	True	99.9822	1441	1442	95	conclusive
Vibrio coralliilyticus	strain=ATCC BAA-450	GCA_000176135.1	190893	190893	type	True	79.8388	467	1442	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.4295	350	1442	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.356	350	1442	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000176235.1	28175	28175	type	True	79.3182	348	1442	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.3182	326	1442	95	below_threshold
Vibrio salilacus	strain=DSG-S6	GCA_002811245.1	1323749	1323749	type	True	79.3161	311	1442	95	below_threshold
Vibrio orientalis	strain=CIP 102891	GCA_000222645.2	28175	28175	type	True	79.1495	337	1442	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	79.1133	251	1442	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	79.0884	238	1442	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	79.057	256	1442	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000024825.1	150340	150340	suspected-type	True	79.0279	248	1442	95	below_threshold
Vibrio alginolyticus	strain=NCTC12160	GCA_900460285.1	663	663	type	True	78.9497	249	1442	95	below_threshold
Vibrio sagamiensis	strain=NBRC 104589	GCA_007990935.1	512650	512650	type	True	78.8924	207	1442	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	78.875	213	1442	95	below_threshold
Vibrio alginolyticus	strain=FDAARGOS_97	GCA_001471275.2	663	663	type	True	78.875	247	1442	95	below_threshold
Vibrio hyugaensis	strain=090810a	GCA_000818435.1	1534743	1534743	type	True	78.8203	247	1442	95	below_threshold
Vibrio sagamiensis	strain=NBRC 104589	GCA_000400425.1	512650	512650	type	True	78.8115	206	1442	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	78.6948	259	1442	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.6845	226	1442	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_002224265.1	672	672	type	True	78.6398	242	1442	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	78.4333	204	1442	95	below_threshold
Vibrio vulnificus	strain=ATCC 27562	GCA_000299635.1	672	672	suspected-type	True	78.4	197	1442	95	below_threshold
Vibrio antiquarius	strain=EX25	GCA_000152485.1	150340	150340	suspected-type	True	78.1475	218	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:18,531] [INFO] DFAST Taxonomy check result was written to GCF_013074385.2_ASM1307438v2_genomic.fna/tc_result.tsv
[2024-01-24 14:39:18,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:18,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:18,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4189c0d0-98dc-47de-823c-e46223784fe8/dqc_reference/checkm_data
[2024-01-24 14:39:18,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:18,578] [INFO] Task started: CheckM
[2024-01-24 14:39:18,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013074385.2_ASM1307438v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013074385.2_ASM1307438v2_genomic.fna/checkm_input GCF_013074385.2_ASM1307438v2_genomic.fna/checkm_result
[2024-01-24 14:39:58,441] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:58,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:58,468] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:58,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:58,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013074385.2_ASM1307438v2_genomic.fna/markers.fasta)
[2024-01-24 14:39:58,470] [INFO] Task started: Blastn
[2024-01-24 14:39:58,470] [INFO] Running command: blastn -query GCF_013074385.2_ASM1307438v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4189c0d0-98dc-47de-823c-e46223784fe8/dqc_reference/reference_markers_gtdb.fasta -out GCF_013074385.2_ASM1307438v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:59,716] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:59,720] [INFO] Selected 22 target genomes.
[2024-01-24 14:39:59,721] [INFO] Target genome list was writen to GCF_013074385.2_ASM1307438v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:59,774] [INFO] Task started: fastANI
[2024-01-24 14:39:59,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg19a6f1e4-327b-4905-bb58-796f149e9621/GCF_013074385.2_ASM1307438v2_genomic.fna.gz --refList GCF_013074385.2_ASM1307438v2_genomic.fna/target_genomes_gtdb.txt --output GCF_013074385.2_ASM1307438v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:24,230] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:24,248] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:24,248] [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_013074385.2	s__Vibrio ostreicida	99.9822	1441	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.53	99.53	0.97	0.97	2	conclusive
GCF_000176135.1	s__Vibrio coralliilyticus	79.848	465	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.33	96.21	0.92	0.87	36	-
GCF_013113835.1	s__Vibrio sp013113835	79.6398	486	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967495.1	s__Vibrio neptunius	79.6174	492	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.83	96.84	0.91	0.89	7	-
GCF_009811315.1	s__Vibrio atypicus	79.604	324	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.15	97.15	0.92	0.92	2	-
GCF_004551525.1	s__Vibrio ouci	79.4881	321	1442	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	79.3422	324	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176235.1	s__Vibrio orientalis	79.3326	346	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000967545.1	s__Vibrio galatheae	79.2427	318	1442	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	79.2404	328	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.52	97.23	0.92	0.89	7	-
GCF_000189255.1	s__Vibrio brasiliensis	79.2177	319	1442	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	79.1294	248	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.95	0.87	0.77	78	-
GCF_001274785.1	s__Vibrio hepatarius	79.1215	316	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.05	98.05	0.92	0.92	2	-
GCF_013114545.1	s__Vibrio sp013114545	79.0038	333	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001048675.1	s__Vibrio diabolicus	78.9389	250	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.98	97.44	0.93	0.90	43	-
GCF_007990935.1	s__Vibrio sagamiensis	78.8968	206	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.95	99.91	0.97	0.96	3	-
GCF_000830505.1	s__Vibrio mytili	78.8706	223	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806575.1	s__Vibrio hepatarius_A	78.8531	318	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.94	98.94	0.97	0.97	2	-
GCF_005281835.1	s__Vibrio profundi	78.8473	228	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224265.1	s__Vibrio vulnificus	78.6642	241	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.11	95.22	0.91	0.85	225	-
GCF_000171815.1	s__Vibrio sp000171815	78.6561	196	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064285.1	s__Vibrio ziniensis	78.4532	203	1442	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 14:40:24,250] [INFO] GTDB search result was written to GCF_013074385.2_ASM1307438v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:24,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:24,256] [INFO] DFAST_QC result json was written to GCF_013074385.2_ASM1307438v2_genomic.fna/dqc_result.json
[2024-01-24 14:40:24,256] [INFO] DFAST_QC completed!
[2024-01-24 14:40:24,256] [INFO] Total running time: 0h1m37s