[2024-01-24 11:36:21,374] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:36:21,377] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:36:21,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgc525c84e-cf90-42f1-8562-36a90c747546/dqc_reference
[2024-01-24 11:36:26,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:36:26,846] [INFO] Task started: Prodigal
[2024-01-24 11:36:26,846] [INFO] Running command: gunzip -c /var/lib/cwl/stg98600a87-9dd2-465a-a08e-01e8cdc3cc40/GCF_016734805.1_ASM1673480v1_genomic.fna.gz | prodigal -d GCF_016734805.1_ASM1673480v1_genomic.fna/cds.fna -a GCF_016734805.1_ASM1673480v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:41,287] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:41,288] [INFO] Task started: HMMsearch
[2024-01-24 11:36:41,288] [INFO] Running command: hmmsearch --tblout GCF_016734805.1_ASM1673480v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc525c84e-cf90-42f1-8562-36a90c747546/dqc_reference/reference_markers.hmm GCF_016734805.1_ASM1673480v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:41,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:41,535] [INFO] Found 6/6 markers.
[2024-01-24 11:36:41,571] [INFO] Query marker FASTA was written to GCF_016734805.1_ASM1673480v1_genomic.fna/markers.fasta
[2024-01-24 11:36:41,571] [INFO] Task started: Blastn
[2024-01-24 11:36:41,572] [INFO] Running command: blastn -query GCF_016734805.1_ASM1673480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc525c84e-cf90-42f1-8562-36a90c747546/dqc_reference/reference_markers.fasta -out GCF_016734805.1_ASM1673480v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:42,202] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:42,207] [INFO] Selected 25 target genomes.
[2024-01-24 11:36:42,207] [INFO] Target genome list was writen to GCF_016734805.1_ASM1673480v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:42,279] [INFO] Task started: fastANI
[2024-01-24 11:36:42,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg98600a87-9dd2-465a-a08e-01e8cdc3cc40/GCF_016734805.1_ASM1673480v1_genomic.fna.gz --refList GCF_016734805.1_ASM1673480v1_genomic.fna/target_genomes.txt --output GCF_016734805.1_ASM1673480v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:37:00,250] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:00,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc525c84e-cf90-42f1-8562-36a90c747546/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:37:00,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc525c84e-cf90-42f1-8562-36a90c747546/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:37:00,260] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:37:00,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:37:00,260] [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
Marivirga atlantica	strain=SM1354	GCA_016734805.1	1548457	1548457	type	True	100.0	1391	1391	95	conclusive
Marivirga lumbricoides	strain=CGMCC 1.10832	GCA_014636295.1	1046115	1046115	type	True	78.2459	214	1391	95	below_threshold
Marivirga sericea	strain=DSM 4125	GCA_900177665.1	1028	1028	type	True	77.7989	177	1391	95	below_threshold
Marivirga tractuosa	strain=DSM 4126	GCA_000183425.1	1006	1006	type	True	77.6441	185	1391	95	below_threshold
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	77.0725	59	1391	95	below_threshold
Roseivirga spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	76.4345	54	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:37:00,262] [INFO] DFAST Taxonomy check result was written to GCF_016734805.1_ASM1673480v1_genomic.fna/tc_result.tsv
[2024-01-24 11:37:00,262] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:37:00,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:37:00,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc525c84e-cf90-42f1-8562-36a90c747546/dqc_reference/checkm_data
[2024-01-24 11:37:00,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:37:00,304] [INFO] Task started: CheckM
[2024-01-24 11:37:00,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016734805.1_ASM1673480v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016734805.1_ASM1673480v1_genomic.fna/checkm_input GCF_016734805.1_ASM1673480v1_genomic.fna/checkm_result
[2024-01-24 11:37:45,030] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:45,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:45,054] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:45,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:45,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016734805.1_ASM1673480v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:45,055] [INFO] Task started: Blastn
[2024-01-24 11:37:45,055] [INFO] Running command: blastn -query GCF_016734805.1_ASM1673480v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc525c84e-cf90-42f1-8562-36a90c747546/dqc_reference/reference_markers_gtdb.fasta -out GCF_016734805.1_ASM1673480v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:45,854] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:45,859] [INFO] Selected 22 target genomes.
[2024-01-24 11:37:45,859] [INFO] Target genome list was writen to GCF_016734805.1_ASM1673480v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:45,890] [INFO] Task started: fastANI
[2024-01-24 11:37:45,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg98600a87-9dd2-465a-a08e-01e8cdc3cc40/GCF_016734805.1_ASM1673480v1_genomic.fna.gz --refList GCF_016734805.1_ASM1673480v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016734805.1_ASM1673480v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:02,196] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:02,208] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:38:02,208] [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_016734805.1	s__Marivirga atlantica	100.0	1391	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014636295.1	s__Marivirga lumbricoides	78.2278	215	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	97.82	97.82	0.87	0.87	2	-
GCF_900177665.1	s__Marivirga sericea	77.8111	177	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183425.1	s__Marivirga tractuosa	77.6441	185	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003973485.1	s__Marivirga sp003973485	77.1504	158	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016679925.1	s__Marivirga sp016679925	77.1015	158	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592965.1	s__Fabibacter spongicola	76.4345	54	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:38:02,209] [INFO] GTDB search result was written to GCF_016734805.1_ASM1673480v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:02,210] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:02,213] [INFO] DFAST_QC result json was written to GCF_016734805.1_ASM1673480v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:02,213] [INFO] DFAST_QC completed!
[2024-01-24 11:38:02,213] [INFO] Total running time: 0h1m41s