[2024-01-24 10:57:24,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:24,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:24,903] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8a9f02a-026f-4ed4-80a0-9efd94b9a270/dqc_reference
[2024-01-24 10:57:26,168] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:26,169] [INFO] Task started: Prodigal
[2024-01-24 10:57:26,170] [INFO] Running command: gunzip -c /var/lib/cwl/stgc80a5ac6-74bf-4b74-bc16-da304ed6976a/GCF_028561335.1_ASM2856133v1_genomic.fna.gz | prodigal -d GCF_028561335.1_ASM2856133v1_genomic.fna/cds.fna -a GCF_028561335.1_ASM2856133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:42,534] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:42,534] [INFO] Task started: HMMsearch
[2024-01-24 10:57:42,534] [INFO] Running command: hmmsearch --tblout GCF_028561335.1_ASM2856133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8a9f02a-026f-4ed4-80a0-9efd94b9a270/dqc_reference/reference_markers.hmm GCF_028561335.1_ASM2856133v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:42,805] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:42,806] [INFO] Found 6/6 markers.
[2024-01-24 10:57:42,842] [INFO] Query marker FASTA was written to GCF_028561335.1_ASM2856133v1_genomic.fna/markers.fasta
[2024-01-24 10:57:42,842] [INFO] Task started: Blastn
[2024-01-24 10:57:42,842] [INFO] Running command: blastn -query GCF_028561335.1_ASM2856133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8a9f02a-026f-4ed4-80a0-9efd94b9a270/dqc_reference/reference_markers.fasta -out GCF_028561335.1_ASM2856133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:43,464] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:43,468] [INFO] Selected 12 target genomes.
[2024-01-24 10:57:43,468] [INFO] Target genome list was writen to GCF_028561335.1_ASM2856133v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:43,477] [INFO] Task started: fastANI
[2024-01-24 10:57:43,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgc80a5ac6-74bf-4b74-bc16-da304ed6976a/GCF_028561335.1_ASM2856133v1_genomic.fna.gz --refList GCF_028561335.1_ASM2856133v1_genomic.fna/target_genomes.txt --output GCF_028561335.1_ASM2856133v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:51,584] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:51,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8a9f02a-026f-4ed4-80a0-9efd94b9a270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:51,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8a9f02a-026f-4ed4-80a0-9efd94b9a270/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:51,596] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:51,596] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:51,597] [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
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	87.9226	744	1087	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	86.4421	734	1087	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	82.4173	712	1087	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	82.0843	754	1087	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	81.928	660	1087	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	80.134	652	1087	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	79.9262	622	1087	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	78.5645	318	1087	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.8838	106	1087	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.0701	52	1087	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.0649	62	1087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:51,598] [INFO] DFAST Taxonomy check result was written to GCF_028561335.1_ASM2856133v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:51,599] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:51,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:51,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8a9f02a-026f-4ed4-80a0-9efd94b9a270/dqc_reference/checkm_data
[2024-01-24 10:57:51,601] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:51,669] [INFO] Task started: CheckM
[2024-01-24 10:57:51,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028561335.1_ASM2856133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028561335.1_ASM2856133v1_genomic.fna/checkm_input GCF_028561335.1_ASM2856133v1_genomic.fna/checkm_result
[2024-01-24 10:58:40,231] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:40,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:40,248] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:40,248] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:40,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028561335.1_ASM2856133v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:40,249] [INFO] Task started: Blastn
[2024-01-24 10:58:40,249] [INFO] Running command: blastn -query GCF_028561335.1_ASM2856133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8a9f02a-026f-4ed4-80a0-9efd94b9a270/dqc_reference/reference_markers_gtdb.fasta -out GCF_028561335.1_ASM2856133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:41,075] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:41,078] [INFO] Selected 10 target genomes.
[2024-01-24 10:58:41,078] [INFO] Target genome list was writen to GCF_028561335.1_ASM2856133v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:41,087] [INFO] Task started: fastANI
[2024-01-24 10:58:41,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgc80a5ac6-74bf-4b74-bc16-da304ed6976a/GCF_028561335.1_ASM2856133v1_genomic.fna.gz --refList GCF_028561335.1_ASM2856133v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028561335.1_ASM2856133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:48,341] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:48,350] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:58:48,350] [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_000952855.1	s__Aequorivita vladivostokensis	87.9226	744	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCF_001573155.1	s__Aequorivita aquimaris	86.4566	733	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	82.9638	708	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_001641085.1	s__Aequorivita soesokkakensis	82.408	712	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCF_007997155.1	s__Aequorivita antarctica	82.0808	754	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCF_016757735.1	s__Aequorivita sp016757735	81.9088	662	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	81.3448	679	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733915.1	s__Aequorivita sp002733915	81.2314	661	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	81.0695	585	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_007997135.1	s__Aequorivita lipolytica	80.1331	651	1087	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:48,352] [INFO] GTDB search result was written to GCF_028561335.1_ASM2856133v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:48,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:48,356] [INFO] DFAST_QC result json was written to GCF_028561335.1_ASM2856133v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:48,356] [INFO] DFAST_QC completed!
[2024-01-24 10:58:48,356] [INFO] Total running time: 0h1m23s