[2024-01-25 19:06:20,642] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:20,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:20,644] [INFO] DQC Reference Directory: /var/lib/cwl/stge139d277-d383-48a2-851f-39b74a3d263a/dqc_reference
[2024-01-25 19:06:21,825] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:21,825] [INFO] Task started: Prodigal
[2024-01-25 19:06:21,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg73e69355-1b63-4ed9-8615-a92a9dfb9ccd/GCF_028561565.1_ASM2856156v1_genomic.fna.gz | prodigal -d GCF_028561565.1_ASM2856156v1_genomic.fna/cds.fna -a GCF_028561565.1_ASM2856156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:35,096] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:35,097] [INFO] Task started: HMMsearch
[2024-01-25 19:06:35,097] [INFO] Running command: hmmsearch --tblout GCF_028561565.1_ASM2856156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge139d277-d383-48a2-851f-39b74a3d263a/dqc_reference/reference_markers.hmm GCF_028561565.1_ASM2856156v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:35,348] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:35,349] [INFO] Found 6/6 markers.
[2024-01-25 19:06:35,376] [INFO] Query marker FASTA was written to GCF_028561565.1_ASM2856156v1_genomic.fna/markers.fasta
[2024-01-25 19:06:35,376] [INFO] Task started: Blastn
[2024-01-25 19:06:35,377] [INFO] Running command: blastn -query GCF_028561565.1_ASM2856156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge139d277-d383-48a2-851f-39b74a3d263a/dqc_reference/reference_markers.fasta -out GCF_028561565.1_ASM2856156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:35,995] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:35,999] [INFO] Selected 31 target genomes.
[2024-01-25 19:06:36,000] [INFO] Target genome list was writen to GCF_028561565.1_ASM2856156v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:36,023] [INFO] Task started: fastANI
[2024-01-25 19:06:36,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg73e69355-1b63-4ed9-8615-a92a9dfb9ccd/GCF_028561565.1_ASM2856156v1_genomic.fna.gz --refList GCF_028561565.1_ASM2856156v1_genomic.fna/target_genomes.txt --output GCF_028561565.1_ASM2856156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:51,939] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:51,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge139d277-d383-48a2-851f-39b74a3d263a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:51,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge139d277-d383-48a2-851f-39b74a3d263a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:51,946] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:06:51,946] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:06:51,946] [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
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	77.2713	64	1090	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.769	58	1090	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.4888	59	1090	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.3566	60	1090	95	below_threshold
Salinimicrobium catena	strain=DSM 23553	GCA_900107495.1	390640	390640	type	True	76.3354	63	1090	95	below_threshold
Salinimicrobium catena	strain=CGMCC 1.6101	GCA_900102915.1	390640	390640	type	True	76.2619	63	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:51,947] [INFO] DFAST Taxonomy check result was written to GCF_028561565.1_ASM2856156v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:51,948] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:51,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:51,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge139d277-d383-48a2-851f-39b74a3d263a/dqc_reference/checkm_data
[2024-01-25 19:06:51,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:51,982] [INFO] Task started: CheckM
[2024-01-25 19:06:51,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028561565.1_ASM2856156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028561565.1_ASM2856156v1_genomic.fna/checkm_input GCF_028561565.1_ASM2856156v1_genomic.fna/checkm_result
[2024-01-25 19:07:31,451] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:31,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:31,467] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:31,467] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:31,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028561565.1_ASM2856156v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:31,467] [INFO] Task started: Blastn
[2024-01-25 19:07:31,467] [INFO] Running command: blastn -query GCF_028561565.1_ASM2856156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge139d277-d383-48a2-851f-39b74a3d263a/dqc_reference/reference_markers_gtdb.fasta -out GCF_028561565.1_ASM2856156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:32,329] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:32,332] [INFO] Selected 20 target genomes.
[2024-01-25 19:07:32,332] [INFO] Target genome list was writen to GCF_028561565.1_ASM2856156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:32,355] [INFO] Task started: fastANI
[2024-01-25 19:07:32,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg73e69355-1b63-4ed9-8615-a92a9dfb9ccd/GCF_028561565.1_ASM2856156v1_genomic.fna.gz --refList GCF_028561565.1_ASM2856156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028561565.1_ASM2856156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:43,399] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:43,406] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:07:43,406] [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
GCA_013214815.1	s__Gilvibacter sp013214815	88.7956	810	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163875.1	s__Gilvibacter sp002163875	81.735	679	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003229235.1	s__Gilvibacter sp003229235	77.5687	52	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gilvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002966125.1	s__Pukyongia salina	77.2736	63	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.9927	64	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827225.1	s__SMXJ01 sp009827225	76.7749	62	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	76.769	58	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002065.1	s__SMXJ01 sp013002065	76.5817	54	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997155.1	s__Aequorivita antarctica	76.4888	59	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002379985.1	s__Marixanthomonas sp002379985	76.1045	71	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	99.95	99.94	0.93	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:43,409] [INFO] GTDB search result was written to GCF_028561565.1_ASM2856156v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:43,410] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:43,413] [INFO] DFAST_QC result json was written to GCF_028561565.1_ASM2856156v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:43,413] [INFO] DFAST_QC completed!
[2024-01-25 19:07:43,413] [INFO] Total running time: 0h1m23s