[2024-01-24 13:57:43,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,189] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,189] [INFO] DQC Reference Directory: /var/lib/cwl/stg4880fda7-4ecc-4562-b971-9f523e252def/dqc_reference
[2024-01-24 13:57:44,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,455] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg996ebf56-60bb-4587-82c3-189ce1c9dfe0/GCF_024347535.1_ASM2434753v1_genomic.fna.gz | prodigal -d GCF_024347535.1_ASM2434753v1_genomic.fna/cds.fna -a GCF_024347535.1_ASM2434753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:57,630] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:57,630] [INFO] Task started: HMMsearch
[2024-01-24 13:57:57,630] [INFO] Running command: hmmsearch --tblout GCF_024347535.1_ASM2434753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4880fda7-4ecc-4562-b971-9f523e252def/dqc_reference/reference_markers.hmm GCF_024347535.1_ASM2434753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,942] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,943] [INFO] Found 6/6 markers.
[2024-01-24 13:57:58,008] [INFO] Query marker FASTA was written to GCF_024347535.1_ASM2434753v1_genomic.fna/markers.fasta
[2024-01-24 13:57:58,009] [INFO] Task started: Blastn
[2024-01-24 13:57:58,009] [INFO] Running command: blastn -query GCF_024347535.1_ASM2434753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4880fda7-4ecc-4562-b971-9f523e252def/dqc_reference/reference_markers.fasta -out GCF_024347535.1_ASM2434753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,848] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:58,848] [INFO] Target genome list was writen to GCF_024347535.1_ASM2434753v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,893] [INFO] Task started: fastANI
[2024-01-24 13:57:58,893] [INFO] Running command: fastANI --query /var/lib/cwl/stg996ebf56-60bb-4587-82c3-189ce1c9dfe0/GCF_024347535.1_ASM2434753v1_genomic.fna.gz --refList GCF_024347535.1_ASM2434753v1_genomic.fna/target_genomes.txt --output GCF_024347535.1_ASM2434753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:12,962] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:12,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4880fda7-4ecc-4562-b971-9f523e252def/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:12,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4880fda7-4ecc-4562-b971-9f523e252def/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:12,973] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:58:12,973] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:58:12,973] [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 kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	100.0	1543	1550	95	inconclusive
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	99.9875	1506	1550	95	inconclusive
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	95.4744	1357	1550	95	inconclusive
Vibrio toranzoniae	strain=Vb 10.8	GCA_001541335.1	1194427	1194427	type	True	95.3807	1337	1550	95	inconclusive
Vibrio toranzoniae	strain=CECT 7225	GCA_900089765.1	1194427	1194427	type	True	95.3608	1354	1550	95	inconclusive
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	89.7862	1209	1550	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	89.748	1271	1550	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	89.678	1264	1550	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	88.7779	1299	1550	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	88.1813	1230	1550	95	below_threshold
Vibrio gallaecicus	strain=VB 8.9	GCA_013416885.1	552386	552386	type	True	82.7142	710	1550	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:12,986] [INFO] DFAST Taxonomy check result was written to GCF_024347535.1_ASM2434753v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:12,987] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:12,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:12,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4880fda7-4ecc-4562-b971-9f523e252def/dqc_reference/checkm_data
[2024-01-24 13:58:12,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:13,060] [INFO] Task started: CheckM
[2024-01-24 13:58:13,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024347535.1_ASM2434753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024347535.1_ASM2434753v1_genomic.fna/checkm_input GCF_024347535.1_ASM2434753v1_genomic.fna/checkm_result
[2024-01-24 13:58:59,686] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:59,687] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:59,706] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:59,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:59,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024347535.1_ASM2434753v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:59,707] [INFO] Task started: Blastn
[2024-01-24 13:58:59,708] [INFO] Running command: blastn -query GCF_024347535.1_ASM2434753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4880fda7-4ecc-4562-b971-9f523e252def/dqc_reference/reference_markers_gtdb.fasta -out GCF_024347535.1_ASM2434753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:00,951] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:00,954] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:00,954] [INFO] Target genome list was writen to GCF_024347535.1_ASM2434753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:00,973] [INFO] Task started: fastANI
[2024-01-24 13:59:00,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg996ebf56-60bb-4587-82c3-189ce1c9dfe0/GCF_024347535.1_ASM2434753v1_genomic.fna.gz --refList GCF_024347535.1_ASM2434753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024347535.1_ASM2434753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:20,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:20,158] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:20,158] [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_008801285.1	s__Vibrio kanaloae	99.9875	1506	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	conclusive
GCF_900089765.1	s__Vibrio toranzoniae	95.3703	1353	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.37	97.69	0.93	0.89	7	-
GCF_002156455.1	s__Vibrio coralliirubri	89.7862	1209	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	96.55	95.77	0.88	0.83	22	-
GCF_002156525.1	s__Vibrio celticus	89.6145	1197	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.2787	99.99	99.99	1.00	1.00	2	-
GCF_000272045.2	s__Vibrio crassostreae_C	89.5972	1244	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_000272105.2	s__Vibrio splendidus_I	89.2463	1208	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394185.1	s__Vibrio sp013394185	88.9312	1252	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001048535.1	s__Vibrio crassostreae	88.9083	1249	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_007858795.1	s__Vibrio sp007858795	88.6317	1244	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316985.1	s__Vibrio sp000316985	88.577	1153	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002875705.1	s__Vibrio sp002875705	88.2683	1193	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.93	99.66	0.96	0.93	9	-
GCF_014878155.1	s__Vibrio lentus	88.2004	1232	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	88.0724	1101	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_002156475.1	s__Vibrio gigantis	88.0574	1219	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_900089855.1	s__Vibrio atlanticus	88.0297	1184	1550	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_014879975.1	s__Vibrio bathopelagicus	87.86	1278	1550	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 13:59:20,160] [INFO] GTDB search result was written to GCF_024347535.1_ASM2434753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:20,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:20,164] [INFO] DFAST_QC result json was written to GCF_024347535.1_ASM2434753v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:20,164] [INFO] DFAST_QC completed!
[2024-01-24 13:59:20,164] [INFO] Total running time: 0h1m37s