[2024-01-24 13:25:30,175] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:30,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:30,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg82947cef-ef5a-4c67-8689-8e9878676d8d/dqc_reference
[2024-01-24 13:25:31,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,488] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e5486de-044f-4de9-bb99-51f0f3fcd203/GCF_030409995.1_ASM3040999v1_genomic.fna.gz | prodigal -d GCF_030409995.1_ASM3040999v1_genomic.fna/cds.fna -a GCF_030409995.1_ASM3040999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:42,426] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:42,427] [INFO] Task started: HMMsearch
[2024-01-24 13:25:42,427] [INFO] Running command: hmmsearch --tblout GCF_030409995.1_ASM3040999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82947cef-ef5a-4c67-8689-8e9878676d8d/dqc_reference/reference_markers.hmm GCF_030409995.1_ASM3040999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:42,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:42,769] [INFO] Found 6/6 markers.
[2024-01-24 13:25:42,811] [INFO] Query marker FASTA was written to GCF_030409995.1_ASM3040999v1_genomic.fna/markers.fasta
[2024-01-24 13:25:42,812] [INFO] Task started: Blastn
[2024-01-24 13:25:42,812] [INFO] Running command: blastn -query GCF_030409995.1_ASM3040999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82947cef-ef5a-4c67-8689-8e9878676d8d/dqc_reference/reference_markers.fasta -out GCF_030409995.1_ASM3040999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:43,620] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:43,623] [INFO] Selected 19 target genomes.
[2024-01-24 13:25:43,623] [INFO] Target genome list was writen to GCF_030409995.1_ASM3040999v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:43,632] [INFO] Task started: fastANI
[2024-01-24 13:25:43,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e5486de-044f-4de9-bb99-51f0f3fcd203/GCF_030409995.1_ASM3040999v1_genomic.fna.gz --refList GCF_030409995.1_ASM3040999v1_genomic.fna/target_genomes.txt --output GCF_030409995.1_ASM3040999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:07,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:07,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82947cef-ef5a-4c67-8689-8e9878676d8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:07,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82947cef-ef5a-4c67-8689-8e9878676d8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:07,961] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:07,961] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:07,961] [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 artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	99.955	1479	1500	95	conclusive
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	88.6681	1148	1500	95	below_threshold
Vibrio coralliirubri	strain=Corallo1	GCA_002156455.1	1516159	1516159	type	True	88.6288	1085	1500	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	88.5333	1163	1500	95	below_threshold
Vibrio celticus	strain=Rd 8.15	GCA_002156525.1	446372	446372	type	True	88.5116	1103	1500	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	88.4755	1114	1500	95	below_threshold
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	87.5003	1140	1500	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	87.4804	1154	1500	95	below_threshold
Vibrio splendidus	strain=NCCB 53037	GCA_001558015.1	29497	29497	type	True	87.3526	1121	1500	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	86.9354	1115	1500	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	86.9339	1082	1500	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	86.8861	1077	1500	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	86.8104	1084	1500	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	86.743	1117	1500	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	86.7336	1031	1500	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	86.7326	1072	1500	95	below_threshold
Vibrio lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	86.6215	1084	1500	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	86.5063	1064	1500	95	below_threshold
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	86.3579	1029	1500	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:07,966] [INFO] DFAST Taxonomy check result was written to GCF_030409995.1_ASM3040999v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:07,967] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:07,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:07,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82947cef-ef5a-4c67-8689-8e9878676d8d/dqc_reference/checkm_data
[2024-01-24 13:26:07,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:08,013] [INFO] Task started: CheckM
[2024-01-24 13:26:08,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409995.1_ASM3040999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409995.1_ASM3040999v1_genomic.fna/checkm_input GCF_030409995.1_ASM3040999v1_genomic.fna/checkm_result
[2024-01-24 13:26:45,759] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:45,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:45,782] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:45,782] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:45,782] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409995.1_ASM3040999v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:45,783] [INFO] Task started: Blastn
[2024-01-24 13:26:45,783] [INFO] Running command: blastn -query GCF_030409995.1_ASM3040999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82947cef-ef5a-4c67-8689-8e9878676d8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409995.1_ASM3040999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:46,913] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:46,917] [INFO] Selected 17 target genomes.
[2024-01-24 13:26:46,917] [INFO] Target genome list was writen to GCF_030409995.1_ASM3040999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:46,927] [INFO] Task started: fastANI
[2024-01-24 13:26:46,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e5486de-044f-4de9-bb99-51f0f3fcd203/GCF_030409995.1_ASM3040999v1_genomic.fna.gz --refList GCF_030409995.1_ASM3040999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409995.1_ASM3040999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:05,794] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:05,815] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:27:05,815] [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_002156455.1	s__Vibrio coralliirubri	88.6282	1084	1500	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	88.511	1103	1500	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	88.2597	1128	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_001557875.1	s__Vibrio splendidus_F	87.7079	1117	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.50	97.50	0.93	0.93	2	-
GCF_000272105.2	s__Vibrio splendidus_I	87.6876	1077	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001558015.1	s__Vibrio splendidus	87.3317	1123	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.85	95.03	0.88	0.83	97	-
GCF_001048535.1	s__Vibrio crassostreae	87.2842	1108	1500	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	87.2819	1080	1500	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	86.8483	1047	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_900089855.1	s__Vibrio atlanticus	86.808	1086	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_005144905.1	s__Vibrio cyclitrophicus	86.757	1099	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.18	99.01	0.95	0.91	87	-
GCF_006333845.1	s__Vibrio tasmaniensis	86.7333	1031	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_002156475.1	s__Vibrio gigantis	86.7326	1072	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.72	97.43	0.95	0.90	3	-
GCF_000316985.1	s__Vibrio sp000316985	86.7068	993	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014879975.1	s__Vibrio bathopelagicus	86.6979	1116	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014878155.1	s__Vibrio lentus	86.622	1084	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	-
GCF_008801285.1	s__Vibrio kanaloae	86.3517	1031	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:05,821] [INFO] GTDB search result was written to GCF_030409995.1_ASM3040999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:05,822] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:05,828] [INFO] DFAST_QC result json was written to GCF_030409995.1_ASM3040999v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:05,828] [INFO] DFAST_QC completed!
[2024-01-24 13:27:05,828] [INFO] Total running time: 0h1m36s