[2023-06-28 13:30:41,753] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:30:41,755] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:30:41,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg75b754cc-29d6-4ad4-9f4a-6a148d5ab911/dqc_reference
[2023-06-28 13:30:42,848] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:30:42,848] [INFO] Task started: Prodigal
[2023-06-28 13:30:42,849] [INFO] Running command: gunzip -c /var/lib/cwl/stg31f8362b-f0cd-414e-b4db-6eefeef6bdf3/GCA_019429335.1_ASM1942933v1_genomic.fna.gz | prodigal -d GCA_019429335.1_ASM1942933v1_genomic.fna/cds.fna -a GCA_019429335.1_ASM1942933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:30:46,388] [INFO] Task succeeded: Prodigal
[2023-06-28 13:30:46,388] [INFO] Task started: HMMsearch
[2023-06-28 13:30:46,388] [INFO] Running command: hmmsearch --tblout GCA_019429335.1_ASM1942933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75b754cc-29d6-4ad4-9f4a-6a148d5ab911/dqc_reference/reference_markers.hmm GCA_019429335.1_ASM1942933v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:30:46,556] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:30:46,557] [INFO] Found 6/6 markers.
[2023-06-28 13:30:46,577] [INFO] Query marker FASTA was written to GCA_019429335.1_ASM1942933v1_genomic.fna/markers.fasta
[2023-06-28 13:30:46,577] [INFO] Task started: Blastn
[2023-06-28 13:30:46,577] [INFO] Running command: blastn -query GCA_019429335.1_ASM1942933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75b754cc-29d6-4ad4-9f4a-6a148d5ab911/dqc_reference/reference_markers.fasta -out GCA_019429335.1_ASM1942933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:30:47,119] [INFO] Task succeeded: Blastn
[2023-06-28 13:30:47,122] [INFO] Selected 10 target genomes.
[2023-06-28 13:30:47,123] [INFO] Target genome list was writen to GCA_019429335.1_ASM1942933v1_genomic.fna/target_genomes.txt
[2023-06-28 13:30:47,132] [INFO] Task started: fastANI
[2023-06-28 13:30:47,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg31f8362b-f0cd-414e-b4db-6eefeef6bdf3/GCA_019429335.1_ASM1942933v1_genomic.fna.gz --refList GCA_019429335.1_ASM1942933v1_genomic.fna/target_genomes.txt --output GCA_019429335.1_ASM1942933v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:30:51,146] [INFO] Task succeeded: fastANI
[2023-06-28 13:30:51,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75b754cc-29d6-4ad4-9f4a-6a148d5ab911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:30:51,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75b754cc-29d6-4ad4-9f4a-6a148d5ab911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:30:51,153] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:30:51,153] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:30:51,153] [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
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	81.699	419	646	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	79.3777	290	646	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	79.0599	296	646	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	78.1007	198	646	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	77.9917	179	646	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.5435	151	646	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.5415	127	646	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.5234	107	646	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:30:51,155] [INFO] DFAST Taxonomy check result was written to GCA_019429335.1_ASM1942933v1_genomic.fna/tc_result.tsv
[2023-06-28 13:30:51,155] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:30:51,156] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:30:51,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75b754cc-29d6-4ad4-9f4a-6a148d5ab911/dqc_reference/checkm_data
[2023-06-28 13:30:51,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:30:51,180] [INFO] Task started: CheckM
[2023-06-28 13:30:51,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019429335.1_ASM1942933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019429335.1_ASM1942933v1_genomic.fna/checkm_input GCA_019429335.1_ASM1942933v1_genomic.fna/checkm_result
[2023-06-28 13:31:07,685] [INFO] Task succeeded: CheckM
[2023-06-28 13:31:07,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:31:07,700] [INFO] ===== Completeness check finished =====
[2023-06-28 13:31:07,701] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:31:07,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019429335.1_ASM1942933v1_genomic.fna/markers.fasta)
[2023-06-28 13:31:07,702] [INFO] Task started: Blastn
[2023-06-28 13:31:07,702] [INFO] Running command: blastn -query GCA_019429335.1_ASM1942933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75b754cc-29d6-4ad4-9f4a-6a148d5ab911/dqc_reference/reference_markers_gtdb.fasta -out GCA_019429335.1_ASM1942933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:08,428] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:08,430] [INFO] Selected 10 target genomes.
[2023-06-28 13:31:08,430] [INFO] Target genome list was writen to GCA_019429335.1_ASM1942933v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:31:08,448] [INFO] Task started: fastANI
[2023-06-28 13:31:08,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg31f8362b-f0cd-414e-b4db-6eefeef6bdf3/GCA_019429335.1_ASM1942933v1_genomic.fna.gz --refList GCA_019429335.1_ASM1942933v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019429335.1_ASM1942933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:31:12,965] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:12,972] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:31:12,972] [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_014859695.1	s__Sulfurimonas sp014859695	83.0905	416	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005217605.1	s__Sulfurimonas crateris	81.7376	415	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829675.1	s__Sulfurimonas sp001829675	81.7237	422	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.77	99.75	0.96	0.96	4	-
GCA_002899765.1	s__Sulfurimonas sp002899765	80.9051	364	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903705.1	s__Sulfurimonas sp903903705	80.2012	195	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829715.1	s__Sulfurimonas sp001829715	80.0101	345	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
GCA_001829785.1	s__Sulfurimonas sp001829785	79.4567	334	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.93	99.89	1.00	1.00	4	-
GCA_002452425.1	s__Sulfurimonas sp002452425	79.3942	219	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.33	99.33	0.89	0.89	2	-
GCF_000012965.1	s__Sulfurimonas denitrificans	79.0601	296	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265455.1	s__Sulfurimonas baltica	78.1124	198	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:31:12,974] [INFO] GTDB search result was written to GCA_019429335.1_ASM1942933v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:31:12,974] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:31:12,976] [INFO] DFAST_QC result json was written to GCA_019429335.1_ASM1942933v1_genomic.fna/dqc_result.json
[2023-06-28 13:31:12,977] [INFO] DFAST_QC completed!
[2023-06-28 13:31:12,977] [INFO] Total running time: 0h0m31s