[2024-01-25 18:56:20,763] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:20,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:20,765] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9f33a9a-b671-4344-b659-9ef5f82e23d2/dqc_reference
[2024-01-25 18:56:21,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:21,878] [INFO] Task started: Prodigal
[2024-01-25 18:56:21,878] [INFO] Running command: gunzip -c /var/lib/cwl/stgec231f7e-2fe1-4637-8508-485bce048327/GCF_030409755.1_ASM3040975v1_genomic.fna.gz | prodigal -d GCF_030409755.1_ASM3040975v1_genomic.fna/cds.fna -a GCF_030409755.1_ASM3040975v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:34,968] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:34,968] [INFO] Task started: HMMsearch
[2024-01-25 18:56:34,968] [INFO] Running command: hmmsearch --tblout GCF_030409755.1_ASM3040975v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9f33a9a-b671-4344-b659-9ef5f82e23d2/dqc_reference/reference_markers.hmm GCF_030409755.1_ASM3040975v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:35,264] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:35,266] [INFO] Found 6/6 markers.
[2024-01-25 18:56:35,313] [INFO] Query marker FASTA was written to GCF_030409755.1_ASM3040975v1_genomic.fna/markers.fasta
[2024-01-25 18:56:35,313] [INFO] Task started: Blastn
[2024-01-25 18:56:35,313] [INFO] Running command: blastn -query GCF_030409755.1_ASM3040975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f33a9a-b671-4344-b659-9ef5f82e23d2/dqc_reference/reference_markers.fasta -out GCF_030409755.1_ASM3040975v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:36,070] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:36,074] [INFO] Selected 14 target genomes.
[2024-01-25 18:56:36,074] [INFO] Target genome list was writen to GCF_030409755.1_ASM3040975v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:36,084] [INFO] Task started: fastANI
[2024-01-25 18:56:36,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgec231f7e-2fe1-4637-8508-485bce048327/GCF_030409755.1_ASM3040975v1_genomic.fna.gz --refList GCF_030409755.1_ASM3040975v1_genomic.fna/target_genomes.txt --output GCF_030409755.1_ASM3040975v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:54,942] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:54,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9f33a9a-b671-4344-b659-9ef5f82e23d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:54,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9f33a9a-b671-4344-b659-9ef5f82e23d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:54,954] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:54,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:54,954] [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 lentus	strain=40M4T	GCA_014878155.1	136468	136468	type	True	99.9451	1856	1966	95	conclusive
Vibrio bathopelagicus	strain=Sal10	GCA_014879975.1	2777577	2777577	type	True	92.1922	1536	1966	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	91.135	1514	1966	95	below_threshold
Vibrio splendidus	strain=DSM 19640	GCA_002737025.1	29497	29497	type	True	91.1266	1490	1966	95	below_threshold
Vibrio splendidus	strain=NCCB 53037	GCA_001558015.1	29497	29497	type	True	91.0686	1494	1966	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_024347315.1	693153	693153	type	True	91.0437	1326	1966	95	below_threshold
Vibrio atlanticus	strain=CECT 7223	GCA_900089855.1	693153	693153	type	True	90.9849	1292	1966	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	90.0093	1324	1966	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_006333845.1	212663	212663	suspected-type	True	89.9219	1273	1966	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	89.5353	1376	1966	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	89.3632	1506	1966	95	below_threshold
Vibrio echinoideorum	strain=NFH.MB010	GCA_004764665.1	2100116	2100116	type	True	89.2521	1466	1966	95	below_threshold
Vibrio coralliirubri	strain=DSM 27495	GCA_024347375.1	1516159	1516159	type	True	89.2389	1442	1966	95	below_threshold
Vibrio cyclitrophicus	strain=LMG 21359	GCA_024347435.1	47951	47951	type	True	88.7663	1351	1966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:54,955] [INFO] DFAST Taxonomy check result was written to GCF_030409755.1_ASM3040975v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:54,956] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:54,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:54,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9f33a9a-b671-4344-b659-9ef5f82e23d2/dqc_reference/checkm_data
[2024-01-25 18:56:54,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:55,014] [INFO] Task started: CheckM
[2024-01-25 18:56:55,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409755.1_ASM3040975v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409755.1_ASM3040975v1_genomic.fna/checkm_input GCF_030409755.1_ASM3040975v1_genomic.fna/checkm_result
[2024-01-25 18:57:36,482] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:36,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:36,500] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:36,501] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:36,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409755.1_ASM3040975v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:36,501] [INFO] Task started: Blastn
[2024-01-25 18:57:36,501] [INFO] Running command: blastn -query GCF_030409755.1_ASM3040975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9f33a9a-b671-4344-b659-9ef5f82e23d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409755.1_ASM3040975v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:37,674] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:37,677] [INFO] Selected 13 target genomes.
[2024-01-25 18:57:37,677] [INFO] Target genome list was writen to GCF_030409755.1_ASM3040975v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:37,703] [INFO] Task started: fastANI
[2024-01-25 18:57:37,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgec231f7e-2fe1-4637-8508-485bce048327/GCF_030409755.1_ASM3040975v1_genomic.fna.gz --refList GCF_030409755.1_ASM3040975v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409755.1_ASM3040975v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:55,099] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:55,108] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:55,108] [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_014878155.1	s__Vibrio lentus	99.9451	1856	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.60	95.56	0.86	0.83	91	conclusive
GCF_002875945.1	s__Vibrio lentus_A	93.2138	1474	1966	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	92.1971	1537	1966	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	91.0741	1493	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.85	95.03	0.88	0.83	97	-
GCF_900089855.1	s__Vibrio atlanticus	90.9889	1292	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	N/A	N/A	N/A	N/A	1	-
GCF_000272405.2	s__Vibrio tasmaniensis_A	90.6085	1255	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	96.5791	97.23	97.01	0.87	0.85	20	-
GCF_002873455.1	s__Vibrio splendidus_J	90.5042	1402	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.45	97.37	0.93	0.92	7	-
GCF_006333845.1	s__Vibrio tasmaniensis	89.9077	1275	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.02	95.02	0.87	0.87	2	-
GCF_000272045.2	s__Vibrio crassostreae_C	89.4199	1371	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_004764665.1	s__Vibrio echinoideorum	89.2537	1466	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_013394185.1	s__Vibrio sp013394185	88.9598	1454	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000316985.1	s__Vibrio sp000316985	88.9482	1304	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144905.1	s__Vibrio cyclitrophicus	88.861	1350	1966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.18	99.01	0.95	0.91	87	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:55,110] [INFO] GTDB search result was written to GCF_030409755.1_ASM3040975v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:55,111] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:55,117] [INFO] DFAST_QC result json was written to GCF_030409755.1_ASM3040975v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:55,117] [INFO] DFAST_QC completed!
[2024-01-25 18:57:55,117] [INFO] Total running time: 0h1m34s