[2024-01-25 18:15:20,575] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:20,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:20,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg24e818fc-8b69-4677-8780-bef544b31874/dqc_reference
[2024-01-25 18:15:21,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:21,814] [INFO] Task started: Prodigal
[2024-01-25 18:15:21,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg71dbb759-f04d-4564-8ea2-858f56c4f1f2/GCF_030410015.1_ASM3041001v1_genomic.fna.gz | prodigal -d GCF_030410015.1_ASM3041001v1_genomic.fna/cds.fna -a GCF_030410015.1_ASM3041001v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:30,915] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:30,915] [INFO] Task started: HMMsearch
[2024-01-25 18:15:30,915] [INFO] Running command: hmmsearch --tblout GCF_030410015.1_ASM3041001v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24e818fc-8b69-4677-8780-bef544b31874/dqc_reference/reference_markers.hmm GCF_030410015.1_ASM3041001v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:31,156] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:31,157] [INFO] Found 6/6 markers.
[2024-01-25 18:15:31,193] [INFO] Query marker FASTA was written to GCF_030410015.1_ASM3041001v1_genomic.fna/markers.fasta
[2024-01-25 18:15:31,193] [INFO] Task started: Blastn
[2024-01-25 18:15:31,194] [INFO] Running command: blastn -query GCF_030410015.1_ASM3041001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24e818fc-8b69-4677-8780-bef544b31874/dqc_reference/reference_markers.fasta -out GCF_030410015.1_ASM3041001v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:31,942] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:31,945] [INFO] Selected 26 target genomes.
[2024-01-25 18:15:31,945] [INFO] Target genome list was writen to GCF_030410015.1_ASM3041001v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:31,960] [INFO] Task started: fastANI
[2024-01-25 18:15:31,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg71dbb759-f04d-4564-8ea2-858f56c4f1f2/GCF_030410015.1_ASM3041001v1_genomic.fna.gz --refList GCF_030410015.1_ASM3041001v1_genomic.fna/target_genomes.txt --output GCF_030410015.1_ASM3041001v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:54,863] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:54,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24e818fc-8b69-4677-8780-bef544b31874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:54,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24e818fc-8b69-4677-8780-bef544b31874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:54,877] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:54,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:54,878] [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 cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	99.9934	1470	1473	95	conclusive
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	81.084	491	1473	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	80.8792	482	1473	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	80.8445	490	1473	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	80.738	485	1473	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	80.6955	522	1473	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	80.629	505	1473	95	below_threshold
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	80.5983	483	1473	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	80.59	498	1473	95	below_threshold
Vibrio gallaecicus	strain=VB 8.9	GCA_013416885.1	552386	552386	type	True	80.5321	526	1473	95	below_threshold
Vibrio gallaecicus	strain=CECT 7244	GCA_024347495.1	552386	552386	type	True	80.5271	550	1473	95	below_threshold
Vibrio gallaecicus	strain=DSM 23502	GCA_005281825.1	552386	552386	type	True	80.5254	527	1473	95	below_threshold
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	80.3929	445	1473	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	80.3594	454	1473	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	80.328	444	1473	95	below_threshold
Vibrio profundi	strain=TP187	GCA_005281835.1	1774960	1774960	type	True	80.139	476	1473	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.5765	373	1473	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	79.4619	324	1473	95	below_threshold
Vibrio ziniensis	strain=ZWAL4003	GCA_011064285.1	2711221	2711221	type	True	79.0447	287	1473	95	below_threshold
Vibrio halioticoli	strain=NBRC 102217	GCA_000496695.1	71388	71388	type	True	79.0386	214	1473	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	78.9636	220	1473	95	below_threshold
Vibrio penaeicida	strain=IFO 15640	GCA_019977755.1	104609	104609	type	True	78.9286	279	1473	95	below_threshold
Vibrio diazotrophicus	strain=NBRC 103148	GCA_000740015.1	685	685	type	True	78.8933	300	1473	95	below_threshold
Vibrio litoralis	strain=DSM 17657	GCA_000426765.1	335972	335972	type	True	78.8187	222	1473	95	below_threshold
Vibrio casei	strain=DSM 22364	GCA_002218025.2	673372	673372	type	True	78.749	207	1473	95	below_threshold
Vibrio plantisponsor	strain=LMG 24470	GCA_013041605.1	664643	664643	type	True	78.6576	330	1473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:54,879] [INFO] DFAST Taxonomy check result was written to GCF_030410015.1_ASM3041001v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:54,880] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:54,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:54,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24e818fc-8b69-4677-8780-bef544b31874/dqc_reference/checkm_data
[2024-01-25 18:15:54,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:54,924] [INFO] Task started: CheckM
[2024-01-25 18:15:54,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030410015.1_ASM3041001v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030410015.1_ASM3041001v1_genomic.fna/checkm_input GCF_030410015.1_ASM3041001v1_genomic.fna/checkm_result
[2024-01-25 18:16:25,422] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:25,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:25,446] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:25,446] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:25,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030410015.1_ASM3041001v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:25,447] [INFO] Task started: Blastn
[2024-01-25 18:16:25,447] [INFO] Running command: blastn -query GCF_030410015.1_ASM3041001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24e818fc-8b69-4677-8780-bef544b31874/dqc_reference/reference_markers_gtdb.fasta -out GCF_030410015.1_ASM3041001v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:26,621] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:26,624] [INFO] Selected 26 target genomes.
[2024-01-25 18:16:26,624] [INFO] Target genome list was writen to GCF_030410015.1_ASM3041001v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:26,641] [INFO] Task started: fastANI
[2024-01-25 18:16:26,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg71dbb759-f04d-4564-8ea2-858f56c4f1f2/GCF_030410015.1_ASM3041001v1_genomic.fna.gz --refList GCF_030410015.1_ASM3041001v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030410015.1_ASM3041001v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:50,952] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:50,973] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:50,973] [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_000272145.2	s__Vibrio sp000272145	98.128	1197	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.26	98.15	0.92	0.92	4	conclusive
GCF_001048535.1	s__Vibrio crassostreae	81.0213	483	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_014878155.1	s__Vibrio lentus	80.9042	490	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_000272045.2	s__Vibrio crassostreae_C	80.7421	497	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_007858795.1	s__Vibrio sp007858795	80.6958	489	1473	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	80.6532	467	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_004764665.1	s__Vibrio echinoideorum	80.5774	493	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_000272105.2	s__Vibrio splendidus_I	80.5681	478	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281825.1	s__Vibrio gallaecicus	80.5337	527	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005281815.1	s__Vibrio chagasii	80.3075	447	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCF_005281835.1	s__Vibrio profundi	80.1596	472	1473	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	79.9073	362	1473	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	79.8821	254	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002877365.1	s__Vibrio sp002877365	79.7803	327	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169995.1	s__Vibrio sp000169995	79.6679	444	1473	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	79.6166	372	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900233005.1	s__Vibrio tapetis	79.5528	326	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827885.1	s__Vibrio renipiscarius	79.4668	321	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000400365.1	s__Vibrio jasicida	79.1178	400	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.91	97.51	0.91	0.89	25	-
GCF_011064285.1	s__Vibrio ziniensis	79.0537	284	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740015.1	s__Vibrio diazotrophicus	78.9132	298	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.42	96.82	0.87	0.85	7	-
GCF_003970425.1	s__Vibrio penaeicida	78.8902	256	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.14	96.14	0.85	0.85	2	-
GCF_000426765.1	s__Vibrio litoralis	78.8487	219	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.36	97.06	0.89	0.86	3	-
GCF_014596725.1	s__Vibrio sp014596725	78.8401	299	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.52	98.52	0.94	0.94	2	-
GCF_015278125.1	s__Vibrio sp015278125	78.7525	334	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013041605.1	s__Vibrio plantisponsor	78.6687	329	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.35	98.35	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:50,984] [INFO] GTDB search result was written to GCF_030410015.1_ASM3041001v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:50,985] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:50,989] [INFO] DFAST_QC result json was written to GCF_030410015.1_ASM3041001v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:50,989] [INFO] DFAST_QC completed!
[2024-01-25 18:16:50,989] [INFO] Total running time: 0h1m30s