[2024-01-24 12:06:35,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:35,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:35,238] [INFO] DQC Reference Directory: /var/lib/cwl/stg0578796f-6037-407e-b851-627eb4bfdb61/dqc_reference
[2024-01-24 12:06:36,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:36,521] [INFO] Task started: Prodigal
[2024-01-24 12:06:36,521] [INFO] Running command: gunzip -c /var/lib/cwl/stge79643b1-431b-45bf-811a-a662eb95c391/GCF_001683355.1_ASM168335v1_genomic.fna.gz | prodigal -d GCF_001683355.1_ASM168335v1_genomic.fna/cds.fna -a GCF_001683355.1_ASM168335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:51,287] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:51,288] [INFO] Task started: HMMsearch
[2024-01-24 12:06:51,288] [INFO] Running command: hmmsearch --tblout GCF_001683355.1_ASM168335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0578796f-6037-407e-b851-627eb4bfdb61/dqc_reference/reference_markers.hmm GCF_001683355.1_ASM168335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:51,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:51,557] [INFO] Found 6/6 markers.
[2024-01-24 12:06:51,589] [INFO] Query marker FASTA was written to GCF_001683355.1_ASM168335v1_genomic.fna/markers.fasta
[2024-01-24 12:06:51,590] [INFO] Task started: Blastn
[2024-01-24 12:06:51,590] [INFO] Running command: blastn -query GCF_001683355.1_ASM168335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0578796f-6037-407e-b851-627eb4bfdb61/dqc_reference/reference_markers.fasta -out GCF_001683355.1_ASM168335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:52,215] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:52,220] [INFO] Selected 8 target genomes.
[2024-01-24 12:06:52,221] [INFO] Target genome list was writen to GCF_001683355.1_ASM168335v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:52,225] [INFO] Task started: fastANI
[2024-01-24 12:06:52,226] [INFO] Running command: fastANI --query /var/lib/cwl/stge79643b1-431b-45bf-811a-a662eb95c391/GCF_001683355.1_ASM168335v1_genomic.fna.gz --refList GCF_001683355.1_ASM168335v1_genomic.fna/target_genomes.txt --output GCF_001683355.1_ASM168335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:01,171] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:01,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0578796f-6037-407e-b851-627eb4bfdb61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:01,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0578796f-6037-407e-b851-627eb4bfdb61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:01,183] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:07:01,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:01,184] [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
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	100.0	1099	1099	95	conclusive
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	99.9878	1096	1099	95	conclusive
Prevotella scopos	strain=DSM 22613	GCA_900129535.1	589437	589437	type	True	99.9213	1025	1099	95	conclusive
Prevotella scopos	strain=JCM 17725	GCA_000614285.1	589437	589437	type	True	99.8768	1002	1099	95	conclusive
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	88.1206	811	1099	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	88.0654	814	1099	95	below_threshold
Prevotella vespertina	strain=A2879	GCA_009728485.1	2608404	2608404	type	True	81.3965	400	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:01,185] [INFO] DFAST Taxonomy check result was written to GCF_001683355.1_ASM168335v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:01,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:01,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:01,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0578796f-6037-407e-b851-627eb4bfdb61/dqc_reference/checkm_data
[2024-01-24 12:07:01,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:01,223] [INFO] Task started: CheckM
[2024-01-24 12:07:01,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001683355.1_ASM168335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001683355.1_ASM168335v1_genomic.fna/checkm_input GCF_001683355.1_ASM168335v1_genomic.fna/checkm_result
[2024-01-24 12:07:47,030] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:47,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:47,048] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:47,049] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:47,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001683355.1_ASM168335v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:47,049] [INFO] Task started: Blastn
[2024-01-24 12:07:47,050] [INFO] Running command: blastn -query GCF_001683355.1_ASM168335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0578796f-6037-407e-b851-627eb4bfdb61/dqc_reference/reference_markers_gtdb.fasta -out GCF_001683355.1_ASM168335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:47,821] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:47,824] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:47,824] [INFO] Target genome list was writen to GCF_001683355.1_ASM168335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:47,829] [INFO] Task started: fastANI
[2024-01-24 12:07:47,829] [INFO] Running command: fastANI --query /var/lib/cwl/stge79643b1-431b-45bf-811a-a662eb95c391/GCF_001683355.1_ASM168335v1_genomic.fna.gz --refList GCF_001683355.1_ASM168335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001683355.1_ASM168335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:55,447] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:55,461] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:55,461] [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_018127785.1	s__Prevotella scopos	99.9878	1096	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.97	1.00	1.00	4	conclusive
GCF_000144405.1	s__Prevotella melaninogenica	88.0499	814	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.46	95.36	0.87	0.78	36	-
GCF_018127925.1	s__Prevotella melaninogenica_C	87.8718	796	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609775.1	s__Prevotella melaninogenica_A	87.8522	778	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018127965.1	s__Prevotella melaninogenica_B	87.5989	796	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.77	95.72	0.91	0.89	4	-
GCF_018128065.1	s__Prevotella sp000467895	87.2291	779	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	96.42	0.91	0.83	4	-
GCF_000257925.1	s__Prevotella sp000257925	81.582	404	1099	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.40	96.99	0.92	0.83	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:55,463] [INFO] GTDB search result was written to GCF_001683355.1_ASM168335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:55,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:55,466] [INFO] DFAST_QC result json was written to GCF_001683355.1_ASM168335v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:55,466] [INFO] DFAST_QC completed!
[2024-01-24 12:07:55,466] [INFO] Total running time: 0h1m20s